Email: Import of the fission yeast revisions from the Broad Institute comparative genome paper into GeneDB
Originally sent by Val Wood to pombelist Sat Apr 23 16:00:37 BST 2011
The changes reported in PMID:21511999 are visible in GeneDB.
Gene Structure Changes
We have imported 306 of the gene structure changes. Some reported
changes were rejected because :
i) The change was already incorporated
ii) The gene is known to be frame-shifted (the correct, albeit gene
structure is currently represented) the confirmed frame-shifts will be
fixed in the next round of sequence changes.
iii) A different start site was reported, but homology or experimental
evidence supports the existing coding sequence start site (if this was
inconclusive I used the Broad start site)
iv) The existing structure was already experimentally supported (in
these cases alternative transcript features will be created once we move
to the new PomBase)
Most of the changes are small, alterations to gene structures and
include mainly:
i) Additional in-frame introns
ii) Use of an alternative starting methionine
iii) Use of an alternative, but proximal acceptor (in these cases it
is possible that both variants occur, but we have used the new
experimentally supported one)
iv) A couple of genes were “un-merged” and one merged.
A small number of changes were larger, and involved additional N or C
terminal exons, and occasionally gross changes to coding sequence.
As there are a large number of changes it is possible that your gene(s)
of interest could be affected.
All of the updated genes are annotated with:
“warning, gene structure updated”PMID:xxxxxxxx” (this will change to
PMID:21511999 when GeneDB is next updated)
in the “controlled curation” section of the gene page
New Genes
New gene structures have been created for the new genes reported
All new genes identified in this analysis are annotated with:
“warning, new gene PMID:xxxxxxxx” (this will change to PMID:21511999
when GeneDB is next updated)
in the “controlled curation” section of the gene page
ncRNAs
All non coding RNAs were imported.
Some are clearly coincident with existing predicted RNAs (However, some
of the previously annotated RNA’s may appear on the incorrect strand as
they were derived from Affymetrix data),
Over time, these will be assessed and merged where appropriate.
UTRs
The UTRs derived from the Broad data have been used for the consensus
UTR set, the precedence for the current annotated consensus set is now :
Individual published sources> PMID:21511999 >PMID:20118936
We hope to make the entire datasets available in the new PomBase.
If you have any questions, please direct them to the new helpdesk,
helpdesk at pombase.ac.uk, or send your query directly using the curator
feedback on the GeneDB web page.
Getting started with PomBase JBrowse
The PomBase genome browser can be accessed in multiple ways:
- On any PomBase page, click the “Search” tab in the header menu, and select “Genome browser”
- From a gene page, click the “View region in JBrowse …” link just above the map image
- On the publication page for any paper with associated datasets, select tracks from the list and click the “Load in JBrowse” button
- Go directly to https://www.pombase.org/jbrowse/
DNA sequence, forward features and reverse features
Tracks for annotated sequence features — genes, repeats, etc. — on the forward and reverse strands are displayed by default.
To show the track containing the reference DNA sequence, use the “Genome sequence and features” filter and enable the “DNA sequence” track as described below.
See this FAQ to display a sequence region using coordinates.
To download sequence, see the “Exporting data” section below (it works the same way as for any other track).
Enabling data tracks
To show data tracks:
Click on the “Select tracks” button in the top left corner.
Locate the track(s) of interest (see below), and then click the tickbox for any individual track to toggle it on/off, or use the tickbox in the header to enable/disable all of the listed tracks at once.
Click the “Back to browser” button at the top.
The tracks should now be displayed. For example, the sequence feature and DNA sequence tracks look like this:
To hide a track, click the (X) button to the left of the track label, or go to the “Select tracks” page and clear its tickbox.
Drag and drop tracks to change the order in which they appear.
Changing the track scale
By default, the scale fits the range of the data being displayed in the current viewing window. The scale can be manually defined.
Click the downarrow to the right of the track label, and click on edit config:
Change the scale by defining a max_score and/or a min score:
The scale can be made consistent across tracks:
jbrowse_rescaled.png
More wiggle track configuration option in the official JBrowse documentation
Locating data
Each entry in the left-hand column can be used to filter the track list. Filter criteria fall into several categories, corresponding to some of the track metadata (see below):
As you select filters, the screen will update to show only relevant criteria on the left, and matching tracks on the right.
You can also search for names, keywords, etc. using the “Contains text” box.
Any applied filters, including text, can be cleared by clicking the red X button that appears next to a selected filter (in the search box or the left-hand column), or by using the “Clear All Filters” button.
For a list of recently enabled tracks, click “Recently Used”.
Track metadata
Information about each track is captured as part of the curation process. Metadata includes:
- Data type: what the experiment measured
- Track label (name): Brief description that appears with the track in the browser display
- Alleles: data from wild type or mutant cells
- Growth phase or response: data from cells assayed a specific stress response or growth phase (e.g. nitrogen starvation, oxidative stress, vegetative growth)
- Localized gene product: the protein assayed in a chromatin binding experiment
- Strain background mutations: any background mutations present in the strain for experimental purposes only and not considered as influencing the results in themselves, such as auxotrophic markers (e.g. leu1-1) or alleles utilized for block and release experiments (e.g. cdc25-22)
- Mating type and ploidy
- Conditions: experimental conditions, e.g. whether cells were grown in YES or EMM, or if H2O2 or t-BOOH was used to induce oxidative stress
- Study ID: accession for the study encompassing the data in external databases (e.g. GEO, ArrayExpress)
- Sample ID: accession for the sample used to generate the data in external databases (e.g. GEO, ArrayExpress)
- First author name
- PubMed ID: paper in which the data were published
- Publication year
The metadata can be viewed in two ways:
In the track selector, tracks are listed with associated metadata on the right hand side:
In the browser, hover over a track label to display a down arrow:
Click the arrow, then click “About this track” in the dropdown menu:
The metadata and stats are displayed:
To dismiss the popup, click the ‘X’ in the upper right corner or the ‘OK’ button at the bottom.
Navigating the browser
Moving around
There are several ways to navigate the genome.
Use the box at the top that displays the chromosomal coordinates to navigate to a specified location:
In the coordinates box,
- Type a gene name, or
- Select a chromosome in the pulldown, then type or paste a range of coordinates (two numbers separated by two dots, e.g. 2323258..2336458).
- If you select one of the pulldown options but omit coordinates, the browser goes to a default location spanning most of the selected chromosome.
- You can also type both a chromosome ID and coordinates directly in the location box, e.g II:2323258..2336458. Use Roman numerals (I, II, III) for the three nuclear chromosomes.
- Click the “Go” button or hit return to go to the gene or region.
- Coordinates for some regions of interest:
- Centromeres
- I:3753687..3789421
- II:1602264..1644747
- III:1070904..1137003
- Mating type region
- II:2129208..2137121
- rDNA (link to one complete repeat)
- III:5542..13722
- Centromeres
- For more information on the chromosome selection options, see PomBase documentation on genome sequencing status, the mating type region, and rDNA.
In the uppermost bar, a red box indicates the size and position of the currently displayed region, in the context of the whole chromosome. Click in the bar or drag the red box to change position.
Use the arrows next to the bar with the box for chromosomal coordinates to move right or left in increments.
Drag or swipe (depending on device) in the main browser window to scroll.
Zooming
To zoom:
Use the + and - buttons, or
In the main browser window, double-click to zoom in, and shift-double-click to zoom out, or
Use the narrow bar below the chromosomal coordinates:
Click and drag to highlight a region, then click within the highlighted region to zoom so the region fills the browser window:
To see the DNA sequence, zoom in until it appears, first as color-coded blocks, and then labeled with letters.
More S. pombe-specific information can be found in the Genome browser FAQ list.
Exporting data
To export the data for any track, hover over the track label to display a down arrow:
Click the arrow, then click “Save track data” in the dropdown menu:
In the popup, choose a data format. DNA sequence is provided in FASTA format. GFF3 is available for most tracks; other options depend on the data type. You can also edit the name of the file where the data will be saved.
Click ‘View’ to see how the data will appear in the saved file. To download the data file click ‘Save’ (available in the original popup or the ‘View’ panel). To dismiss the popup withous saving, click the ‘X’ in the upper right corner or the ‘Close’ button at the bottom.
Email: Annotated transcription start and termination sites for fission yeast.
Originally sent by Val Wood to pombelist Fri Feb 4 12:08:34 GMT 2011
A set of genome wide transcription start and termination sites manually
annotated by Lantermann et. al in PMID: 20118936, based on
transcriptome data from Dutrow et. al. PMID: 18641648 have been used to
create 5’ and 3’UTR features for the reference genome, for genes with no
previously annotated transcript from another source.
This increases the number of manually annotated UTRs from
298 to 3605 for 5’
778 to 3693 for 3’
Because it appears that transcription start and end can be fuzzy,
these features should be considered as an “indicator” of the likely
extent of transcription. We will continue to revise the reference
transcript set as updates are reported, to represent the longest
discrete transcript for a region as the consensus.
Data Access
You can access the transcription start and end from individual GeneDB
gene pages for genes of interest using the sequence viewers GBrowse or
Artemis. The links to these 2 browsers are to the right and left of the
“context map” on the “Location” section of the gene page.
(Artemis tips: Use the “Artemis applet” option selected; If you are
interested in a specific gene, reduce the upstream and downstream range
of to 1000 before clicking “submit”; the page will take a few seconds
to render the first time in a session)
You can download this data as part of the complete annotation in the “rich EMBL files” from here: ftp://ftp.sanger.ac.uk/pub/yeast/pombe/Chromosome_contigs/ (the files chromosome*.contig) and view them in Artemis on your desktop (see the Artemis FAQ and the Artemis manual (pdf; Sanger site) for additional information).
Hosting Further Transcriptome Datasets
Clearly, as more transcriptome data becomes available the community will
require access to the different datasets, in addition to the consensus
transcripts. We intend to provide this in the future through the new
PomBase using the Ensembl viewer.
Advanced search
Note: This documentation is still a work in progress. Please contact the helpdesk if you have any questions.
The PomBase advanced search allows you to construct complex queries for S. pombe genes. At present all advanced search results are lists of genes that match the query specifications. Hints for specific searches are available in the PomBase FAQ, and linked below (scroll down to Search tips).
Overview
In the Search menu, choose Advanced (or bookmark https://www.pombase.org/query).
In the Query panel (top), click one of the links in the list on the left to choose a query type (described below). Arrowheads indicate list entries that expand to offer two or more query types, organized in tabs. For each query, the interface guides your input.
In the History panel (bottom), queries are listed in reverse chronological order (most recently run first). Results are linked in the Count column; the link goes to a page that displays the gene name, systematic ID, and product description for matching genes. The Download button offers additional options, including nucleotide and (where applicable) protein sequence. To return to the search page, use the blue “<- Advanced search” button just above the result list, not your browser’s “Back” button.
You can select queries in the list to combine or delete them. To combine queries, you must select two or more from the list, and then click one of the operator buttons:
Results are added to the history list:
Queries using the NOT operator default place the more recently run query first (newer NOT/Subtract older):
Click “Change direction” to switch the order. Click “Submit” to run the query.
You can also move any query to the top of the history list by clicking its “Results” link, and then clicking the “<- Advanced search” button.
Query results can remain available in the history list for several days. If changes in annotation cause results to change since a query was last run, an additional “Previous” column will be displayed in the history list, showing the out-of-date result count:
Click on the “Results” link to re-run the query and retrieve the up-to-date result.
If the parameters for a query are not all visible in the history, a “[details]” toggle (1) to show or hide additional details will appear. You can also edit the name that appears in the history list (2). The name will be used as part of the description when the query is used in any combined query (which can, in turn, be given a new name).
Query results page
Clicking on any up-to-date count in the “Results” column goes to a page that shows the count, query details, and a list of matching genes.
Return to the main Advanced search page (you can also use the browser “back” button)
Click on a header to sort by the column
Select columns to display. A set of gene expression data sets are hidden by default; click “Show gene expression columns” to reveal the additional options.
Select from the pulldown to send the gene list to QuiLT for visualisation, or, for lists of up to 150 genes, see the genes highlighted in violin plots of quantitative expression datasets. (At present data from Marguerat S et al. (2012) and Carpy A et al. (2014) are included.)
Show GO slim annotations for genes in the list. Click “Slim with” to reveal a dropdown, and choose a slim. Note: when you return to the main Advanced search page, the query history will include an entry showing the query as a gene list. This is harmless.
Narrow the list: click the button to reveal checkboxes. Available for lists of up to 1000 genes.
Download selected data for genes in the list. The popup offers three sets of options:
- The default “Tab delimited” view offers a set of details that can be included in a downloaded text file. Click “Show gene expression columns” to reveal additional options.
- Use the “Sequence” tab to retrieve amino acid or nucleotide sequences in FASTA format. Use the checkboxes to select which items are included in the headers. When “Nucleotide” is selected, flanking sequence options similar to those on the gene page are available.
- In the “GO Annotation” tab, you can choose which ontologies to include. Downloaded annotations are in GAF 2.1 format. Note that only “direct”, not inferred, annotations are included, as described in this FAQ.
Sharing search results
Each results page has a stable, unique URL that you can bookmark, copy/paste, and share. Anyone who follows a shared link will see the same results page, and the query will be added to their query history.
The “Visualise” and “Slim” options also generate stable, unique, sharable URLs.
Query types
Ontology queries (GO, phenotype, protein modification, and protein sequence feature) retrieve genes that are annotated to the selected term(s), and to their descendants via specified relations (see the GO documentation on Ontology Structure and Ontology Relations for more information on relationships between terms in ontologies, and see the descriptions below of specific ontology filters for lists of which relations are followed to retrieve annotations). Ontologies can be searched by ID or term name. Type or paste a complete ontology ID, including the prefix (e.g. GO:0005634, FYPO:0002059), or simply start typing to search for a term name. Choose a term from the list of options offered by the autocomplete, and click “Submit”.
Note: Only terms that are used in annotations (direct or inferred by transitivity) will appear as autocomplete suggestions. This is to avoid having irrelevant terms, such as “chloroplast” or “echolocation” appearing. Any term without annotations can be found by searching by its ID, and will appear in the query history with “0” results.
Commonly used queries
This item offers convenient links to perform frequently used queries easily. Click on the query description to add the results to the query history.
Please contact the helpdesk if you would like any queries added to the selection.
Gene names and IDs
Type or paste a list of gene names or systematic IDs (or a mixture), or click the “Browse” button to select a file to upload. Click “Lookup” to add the gene list to the history (useful for combining the list with other queries).
UniProt accessions
Links to the Identifier Mapper.
GO
The Gene Ontology (GO) query retrieves gene products annotated to a GO term and to any of its child terms, following the is_a, part_of, regulates, positively_regulates,and negatively_regulates relationships in the ontology. You may also find it helpful to search or browse in QuickGO or AmiGO to find GO terms of interest. If one search does not seem to retrieve as many results as you expect, try again using a less specific term. Note: prior to the November 2014 PomBase release, the regulates relations were not followed, and PomBase GO search results therefore did not match those in AmiGO.
Phenotype
The phenotype (Fission Yeast Phenotype Ontology) query retrieves genes annotated to a FYPO term and to any of its child terms, following the is_a, part_of, output_of, has_output, and has_part relationships in the ontology. This query also offers additional context-dependent options. By default, the phenotype search retrieves genes from single-allele haploid and diploid genotypes annotated to the searched FYPO term:
You can alter the selected options to add genes from multi-allele genotypes, and/or to search specifically for haploids or diploids. See the gene page phenotype documentation and the genotype page documentation for more information.
If you select single-locus haploids, expression level options are also available:
Different alleles of one gene may have different phenotypes, and one allele may give rise to different phenotypes under different experimental conditions. At present, you can retrieve annotations for all alleles of a gene, or use the “Expression level” options restrict the query to null alleles (covers deletions and any other sequence changes, such as most disruptions, that completely abolish expression of the gene) or overexpression of the wild type allele.
The “Constrain condition” option restricts the results to include only genes that have phenotype annotations including the specified condition. The search uses the same condition descriptors as Canto and the PomBase web pages. Start typing, then choose from the autocomplete options.
Note that the results will include any gene that has phenotype annotations including the specified condition for any allele. Queries that include conditions can be combined using the AND, NOT, or OR operators like any other, but the result of any combination of phenotype queries will likely include annotations for different alleles. There may not be any individual annotation in which both/all of multiple conditions co-occur.
The search does not yet support querying for multiple conditions on the same annotation, nor for queries that exclude a given condition; both are planned for future development.
Disease
Search the Monarch Disease Ontology to find S. pombe genes whose human orthologs have been implicated in disease. Start typing ‘disease’ or the name of a specific disease, and choose from the autocomplete options. To retrieve all disease-associated genes, type or paste “MONDO:0000001”.
Product type
Choose a gene product type (e.g. protein coding, tRNA, etc.) from the pulldown menu.
Protein modification
Search for terms or IDs in the PSI-MOD ontology.
Domain, features and motifs
Queries for proteins that have a specified domain, sequence feature, or structural feature
Domain ID
Search for a protein domain using an ID from Pfam, PRINTs, PROFILE, ProSite, or InterPro. Type or paste an accession and click “Submit”.
Protein motifs
This query searches for terms or IDs in the Sequence Ontology and retrieves protein-coding genes where the protein has the feature represented by the SO term (e.g. KEN box SO:0001807).
TM domains
Find protein-coding genes with products that have a specified number of transmembrane domains. Use the appropriate button for any TM domains or none, or enter the desired minimum and maximum number and click “Search”.
Coiled-coil regions
Find protein-coding genes with products that have a specified number of coiled-coil regions. Use the appropriate button for any coiled-coil regions or none, or enter the desired minimum and maximum number and click “Search”.
Disordered regions
Find protein-coding genes with products that have a specified number of disordered regions. Use the appropriate button for any disordered regions or none, or enter the desired minimum and maximum number and click “Search”.
Low-complexity regions
Find protein-coding genes with products that have a specified number of low-complexity regions. Use the appropriate button for any low-complexity regions or none, or enter the desired minimum and maximum number and click “Search”.
Protein properties
Physical properties of protein gene products:
Protein length
Find protein-coding genes with products in a specified length range. Enter the desired minimum and maximum length and click “Search”.
Protein mol. weight
Find protein-coding genes with products in a specified mass range. Enter the desired minimum and maximum mass in kiloDaltons (kDa) and click “Search”.
Genome location
Find genes in a specified region of a chromosome. Select a chromosome from the pulldown, and click “Search” to retrieve all genes on the chromosome. Or click the radio button to switch to “Genes overlapping range”, and enter start and end coordinates in the boxes to retrieve only genes in the specified region. Note that genes that partly overlap the entered coordinates will be included.
Number of exons
Find genes with a specified number of coding exons in the primary transcript (note: at present this query does not consider any annotated alternative transcripts). Enter the desired minimum and maximum number and click “Search”.
Number of transcripts
Find genes with a specified number of annotated transcript isoforms; Enter the desired minimum and maximum number and click “Search”. (Note: alternative transcripts are only explicitly annotated if functional differences between isoforms are identified- see the browser datasets for the full extent of known transcript variation)
Orthologs and conservation
Taxonomic conservation
Choose one of the descriptions from the pulldown menu. See the gene page documentation for more information.
Protein with orthologs
Choose a species from the pulldown menu to retrieve all S. pombe genes with a curated ortholog in the selected species.
Characterisation status
Choose one of the descriptions from the pulldown menu. See the gene characterisation page for more information.
Search tips
FAQ entries relevant to using the advanced search are organised here by topic. Several of the topics also correspond to gene page sections.
Phenotype searches
- Can I get a list of essential pombe genes?
- How can I find all of the genes that have a given mutant phenotype?
- Why are some genes annotated to both viable and inviable phenotypes?
- How can I browse the phenotype ontology (FYPO)?
Gene Ontology searches
- How can I search or browse GO annotations?
- How can I find genes with a specific activity?
- How can I find protein localization data?
- How can I identify all of the genes that affect a process? (also relevant to phenotype searches)
- Can I retrieve functional annotations for genes in a list?
- How can I find transcription factors and their targets in PomBase?
Protein searches
- How can I find modifications for my protein of interest?
- How can I find all S. pombe proteins in a particular protein family?
- How can I find proteins that have transmembrane domains?
Taxonomic conservation
- How can I find S. pombe genes associated with human disease?
- How can I find all S. pombe genes that are conserved in human?
- Can I search for genes based on conservation in different taxa?
- Can I find all of the unconserved (orphan) genes in fission yeast?
Gene and genome searches
- How can I retrieve all S. pombe genes?
- How can I retrieve all S. pombe protein-coding genes?
- Can I provide a list of genes to search on?
- Can I search for a gene list and retrieve results in the same order as in the input list? (answer: no)
- How can I find snoRNA genes?
- How can I find transposons in the S. pombe genome?
- How can I find genes in a region using chromosome coordinates?
- How can I retrieve intron coordinates or sequences?
- How can I find all sequence features in a region using chromosome coordinates?
- How can I find genes in a region using chromosome coordinates?
Annotation extension relation display
Annotation extensions are used to provide additional specificity for annotations to GO, FYPO, and protein modification annotations. Each extension consists of a relation and another “entity”, which may be a gene in PomBase or another database, or another ontology term. (The GO Consortium wiki page on annotation extensions contains useful information on relations.) Because some relations have unwieldy names, the PomBase gene page display substitutes more readable text.
This table shows the underlying relation name and corresponding display text for the affected relations, and the reciprocal relation displayed in “Target of” annotations (derived from extension data):
| Relation name | Display name | Reciprocal |
|---|---|---|
| activated_by | activated by | N/A |
| coincident_with | at | N/A |
| during | during | N/A |
| exists_during | during | N/A |
| happens_during | during | N/A |
| has_regulation_target | regulates | regulated by |
| in_absence_of | in absence of | N/A |
| in_presence_of | in presence of | N/A |
| inhibited_by | inhibited by | N/A |
| not_exists_during | except during | N/A |
| not_happens_during | except during | N/A |
| occurs_at | at | N/A |
| occurs_in | in | N/A |
| required_for | required for | N/A |
For some relations, the best display string depends on term and its ancestry, as indicated in these tables:
The display for FYPO extensions indicating genes used in assays depends on whether the phenotype is normal or abnormal:
| Relation name | If descendant of | Display name | Reciprocal |
|---|---|---|---|
| assayed_using | FYPO:0001985 abnormal phenotype | affecting | affected by mutation in |
| assayed_enzyme | FYPO:0001985 abnormal phenotype | affecting activity of | activity affected by mutation in |
| assayed_substrate | FYPO:0001985 abnormal phenotype | affecting substrate | affected by mutation in |
| assayed_using | FYPO:0000257 normal phenotype | affecting | N/A (normal means no effect to report in “Target of” section) |
| assayed_enzyme | FYPO:0000257 normal phenotype | affecting activity of | N/A (normal means no effect to report in “Target of” section) |
| assayed_substrate | FYPO:0000257 normal phenotype | affecting substrate | N/A (normal means no effect to report in “Target of” section) |
GO annotation extensions display for part_of:
| If descendant of | Display name | Reciprocal |
|---|---|---|
| GO:0003674 molecular_function | involved in | N/A |
| GO:0008150 biological process | part of | N/A |
The display for the “input” relations (has_input or has_direct_input) follows this pattern:
| If descendant of | Display name | Reciprocal |
|---|---|---|
| GO:0003824 catalytic activity | has substrate | substrate of |
| GO:0006810 transport | transports | transported by |
| GO:0005215 transporter activity | transports | transported by |
| GO:0000976 transcription regulatory region sequence-specific DNA binding | regulates transcription of | transcription regulated by |
| GO:0001216 DNA-binding transcription activator activity | activates transcription of | transcription activated by |
| GO:0001217 DNA-binding transcription repressor activity | represses transcription of | transcription repressed by |
| GO:0003713 transcription coactivator activity | activates transcription of | transcription activated by |
| GO:0003714 transcription corepressor activity | represses transcription of | transcription repressed by |
| GO:0030234 enzyme regulator activity | regulates | regulated by |
| GO:0008047 enzyme activator activity | positively regulates | positively regulated by |
| GO:0004857 enzyme inhibitor activity | negatively regulates | negatively regulated by |
| GO:0051179 localization | localizes | localized by |
| GO:0005488 binding | binds | binds |
| (anything not listed above) | has input | input for |
PomBase displays also use human-friendly names for Protein Ontology (PRO) terms used in extensions (inculding “active form”). The display names include modification positions denoted with these abbreviations:
| Abbreviation | Meaning |
|---|---|
| Ac | acetylated |
| Clv | cleaved (residue specification optional) |
| DiUbiq | diubiquitinated |
| GDP+ | GDP-bound |
| GTP+ | GTP-bound |
| HyperOx | hyperoxidized |
| InitMet- | initiator methionine removed |
| Ip | prenylated |
| Me | methylated |
| Me2 | dimethylated |
| Me3 | trimethylated |
| MonoUbiq | monoubiquitinated |
| Ox+ | oxidized form |
| Phos | phosphorylated (specified residue) |
| PhosRes+ | phosphorylated (unspecified residue) |
| PhosRes- | unphosphorylated (unspecified residue) |
| PolyUbiq | polyubiquitinated |
| Red+ | reduced form |
| Sumo | sumoylated |
| Ubiq | ubiquitinated (residue specification optional) |
| UnMod | unmodified (residue specification optional) |
| UnPhos | unphosphorylated (residue specification optional) |
| UnUbiq | unubiquitinated |
PomBase controlled curation
Gene and publication pages include manually curated annotations of several types that cannot be represented using available ontologies.
For each annotation, the summary view shows a text description, which corresponds to an entry in the internal PB term set. The detailed view adds the PBO ID, evidence (if available), reference, and count. The count links to the ontology term page for the description.
Links in the left-hand navigation menu include:
Complementation - Indicates that an S. pombe gene complements, or is complemented by, a gene from another species
Miscellaneous
Subunit composition - Brief description of homo- or heteromeric complex(es) in which the gene product is found
Warnings - Alerts to changes or anomalies that can affect interpretation of experimental results, such as changes to the sequence or feature annotation
In the Miscellaneous category, annotations fall under one of these sub-headings:
Catalytic activity attributes: Features of a gene product’s catalytic activity, such as KM, kcat, substrate specificity
Experimental tools: Indicates that the gene or its product is used as an experimental tool (e.g. reporter gene construct, selectable marker, antibody)
Genome organization: Attributes of the genomic region around the gene, e.g. duplications, repeats, alternative transcripts
Miscellaneous functional group: Function-related descriptions that are not covered by GO molecular function or biological process annotations
Comment: Experimental observations and other notes that do not fit into ontologies or any of the above controlled curation categories; truly miscellaneous but interesting information
HTP sequence-linked data submission instructions
PomBase welcomes submissions of published HTP sequence-linked data, suitable for viewing in a genome browser. We require JBrowse compliant data files and associated metadata descriptions. Please see the FAQ on file formats for links to the file format descriptions, and other entries in the data submission FAQ category for more information.
Data files
All features in data files need to use these chromosome IDs:
- I
- II
- III
- chr_II_telomeric_gap
- mitochondrial
- mating_type_region
Metadata
We have devised a file format for the metadata we need, with downloadable spreadsheet templates available in Excel and Open Document Format (links may download files, depending on your browser). Letters in the table below refer to spreadsheet columns.
If you prefer, you can prepare a file without using the template. Create a tab-delimited text file, and include a header line that labels the columns, using the entry in the Contents column below as the column header text.
File columns
| Column | Contents | Example | Mandatory? | Multiple entries allowed? |
|---|---|---|---|---|
| 1 (A) | Data type | Transcripts, Chromatin binding, Nucleosome positioning, Poly(A) sites, Replication origins | Yes | No |
| 2 (B) | Track label | see below for format and examples*** | Yes | No |
| 3 (C) | Assayed gene product | Fkh2 | Only required for chromatin binding data, to specify the protein binding to chromatin | No |
| 4 (D) | Strain background | h- cdc25-22, leu1-1 | Yes | Yes |
| 5 (E) | WT or mutant (strains with only background mutations are considered WT) | WT | Yes | No |
| 6 (F) | Mutant alleles | clr4delta, dfp1-3A | No | Yes |
| 7 (G) | Conditions | YES, high temperature; glucose MM, standard temperature + HU | No | No |
| 8 (H) | Comment | free-text field for additional information | No | Yes |
| 9 (I) | Growth phase or response | vegetative growth, meiosis, quiescence, glucose starvation, oxidative stress, heat shock | Yes | Yes if the track combines data |
| 10 (J) | Strand | forward, reverse | No | No |
| 11 (K) | Assay type | tiling microarray, RNA-seq, HT sequencing | Yes | No |
| 12 (L) | First author (surname) | Soriano | Yes | No |
| 13 (M) | Publication year | 2020 | Yes | No |
| 14 (N) | PubMed ID | 31077324 | Yes | No |
| 15 (O) | Database | GEO, ArrayExpress | Required for data available in public repository databases | No |
| 16 (P) | Study ID | GSE110976, PRJEB7403 | Required if the Database column has an entry | No |
| 17 (Q) | Sample ID | GSM3019628, ERS555567 | No | Yes |
| 18 (R) | Data file type | bigwig, bed | Yes | No |
| 19 (S) | File name | name given to submitted data file relevant to the track | Yes | No |
Track label format
The track label must uniquely describe each track. For consistency in track label descriptions, please follow the recommended format as closely as possible:
“Assayed gene product” “Data type” “in mutant” “during Growth phase or response” “additional experimental detail of importance (Conditions, Strain background)” “; repeat” “(strand)” “- First author (Publication year)”
Examples:
- Nucleosome positioning during vegetative growth; repeat 1 - Gonzalez et al. (2016)
- Poly(A) sites during meiosis (forward strand) - Schlackow et al. (2013)
- Transcripts in atf1delta (forward strand) - Soriano et al. (2013)
- Replication origins in cells synchronized by cdc25-ts block/release and hydroxyurea arrest - Xu et al. (2012)
- Replication origins in cells synchronized by elutriation and hydroxyurea arrest - Xu et al. (2012)
- Replication origins in dfp1-3A synchronized by elutriation and hydroxyurea arrest - Xu et al. (2012)
- Transcription start sites during oxidative stress (reverse strand) - Thodberg et al. (2018)
Submit
To submit the files, or if you have any questions, please contact the PomBase curators.
Gene page: Disease associations
The Disease association section lists disease descriptions from the Monarch Initiative’s Mondo Disease Ontology (Mondo) for fission yeast orthologs of human disease-causing genes.
The summary view shows slim terms (see below) and the names of the most specific terms used to annotate the gene.
The detailed view shows more information for each annotation, and may display additional terms:
Mondo slim terms applicable to the gene.
The Mondo term ID and name, which link to a page with additional information, including the term definition, any synonyms, relationships to other Mondo terms, and annotations to the term or its descendants.
Indicates whether the annotation was created by PomBase curators or obtained from an external source (usually Malacards
The paper from which the annotation comes.
The number of genes annotated to the term, linked to an ontology term page as described above.
Gene page: Basic information
At the top of each gene page is a set of basic information about the gene:
- See the Gene Name Registry for more information about S. pombe gene names. Synonyms include all names other than the standard name that have been published for a gene, and thus are not guaranteed to be unique.
- Free text description of the gene product
- Chromosome coordinates for the gene. For protein-coding genes, the “coding start to stop” numbers give the start, end, and length excluding UTRs but including introns (other than introns located entirely within UTRs). The second set of numbers indicate the gene start, end, and length including the default UTRs chosen by PomBase curators (see this FAQ for more information).
- What the three-letter acronym stands for; where available, name descriptions are provided for synonyms as well as primary names.
- Category describing how well-studied a gene is; see the Gene Characterisation page for details. Note: at present this is used in PomBase for S. pombe, but not in JaponicusDB.
- Indicates whether a gene encodes protein, specifies a non-coding RNA, or is a pseudogene
- The size of the mature gene product. For protein-coding genes, the length (number of amino acid residues) and molecular weight are shown.
- Interactive graphic from PomBase JBrowse, centred on the location of the gene. Drag to scroll left and right, double-click to zoom in, shift-double-click to zoom out, and click a feature to see details in a popup. The “Full-screen view” link in the corner opens the fully functional JBrowse in a new tab or window. Reloading a gene page restores the display to the default location and zoom level.
- Links to gene pages for nearby genes
Gene page: External references
The External references section of a gene page provides links to information on a gene or its product in each of several external databases. For each database, a category, the name and a brief description are shown, and the identifier used by the database is displayed and linked.
The resources linked in this section cover a wide range of databases and data types. Because all are external, PomBase staff cannot provide assistance with any of the resources other than problems with the actual links.
Gene page: Gene expression
The Gene expression section of a gene page displays curated qualitative and quantitative information about the level and timing of the gene’s expression. In each subsection, a simple summary appears by default:
- Qualitative descriptions are drawn from a small internal controlled vocabulary, with supporting extensions. Each description links to a list of all genes annotated to the same term.
- a) The expression description name.
- c) An optional extension indicating that expression is observed during a particular process or phase (using GO terms) or in the presence of a particular chemical (using ChEBI terms).
- Quantitative expression data include the number of RNA or protein molecules measured per cell, and may optionally include a copy number range. Quantitative expression annotations also indicate whether the experiment measures expression in a population or a single cell, and usually include a brief description of experimental conditions, drawn from a small ontology maintained by PomBase curators.
- h)What was measured, i.e. RNA or protein.
- i) Molecules per cell (RNA or protein, as indicated in the sub-header). For population-scale experiment types this is an average, whereas for single-cell scale experiments it is an absolute number.
- j) The life cycle stage or cell cycle phase in which expression was measured.
- Click to see the gene highlighted in violin plots of quantitative expression datasets that include it. (At present data from Marguerat S et al. (2012) and Carpy A et al. (2014) are included.)
Click “Show details” to reveal additional information:
- Qualitative expression details:
- a, b) The unique ID and name for the expression description.
- c) Optional extension, as in the summary view.
- d) A brief descriptor for the type of evidence that supports the annotation. The evidence categories come from the Evidence Ontology (ECO).
- e) The display can be filtered to show subsets of the total set of annotations. Choose a cell cycle phase from the “During” pulldown, or throughput from the second pulldown (options that match no annotations are greyed out).
- f) The paper from which the annotation comes.
- g) The number of genes annotated to the description (not including extensions), linked to a list of the genes.
- Quantitative expression details:
- h)What was measured, i.e. RNA or protein.
- i) Molecules per cell, as in the summary view.
- j) The life cycle stage or cell cycle phase in which expression was measured.
- k) Information about experimental conditions, such as temperature, type of medium used, etc. Descriptions come from a small ontology maintained by PomBase curators.
- l) Whether the experiment was done at the level of a single cell or a population of cells.
- m) A brief descriptor for the type of evidence that supports the annotation. The evidence categories come from the Evidence Ontology (ECO). If a more specific description is not available, the general term “experimental evidence” is shown.
- n) The paper from which the annotation comes.
Important: Note that the condition descriptions are rather broad, and therefore do not necessarily capture all details of every aspect that may affect gene expression. We are also unable to capture strain details at present. We therefore recommend consulting the papers cited for the data before comparing or combining data from different publications.
Several of the External References also link to gene expression data.
Gene page: Gene Ontology
PomBase uses the Gene Ontology (GO) to describe the biological context of genes.
GO consists of three distinct ontologies (or sets of vocabularies) that describe a gene’s:
- Molecular Function (MF) — single-step activities such as kinase activity or transporter activity
- Biological Process (BP) — a series of functions with a common goal such as MAPK cascade or cytokinesis
- Cellular component (CC) — the location where the gene product can be found, and what complexes it is part of, for instance nucleus or fatty acid synthase complex
A gene product may be annotated to several GO terms from each of the three ontologies; mcm3, for instance, is annotated to single-stranded DNA helicase activity, ATP binding, and DNA replication origin binding (MFs), it acts in mitotic DNA replication initiation and negatively regulates the MCM helicase activity (BPs), and is found locations including the replication fork and the pre-replicative complex (CC).
Each table includes ontology term details and supporting data. The GO annotation display on PomBase gene pages includes ontology term details and supporting data. The summary view shows just the essentials: The list of terms is filtered, using the ontology structure, so that it shows only the most specific terms used to annotate a genotype, and each unique combination of gene, GO term, and extension(s) is shown once:
- The GO term name, which links to a page with additional information, including the term definition, any synonyms, relationships to other GO terms, and annotations to the term or its descendants. (See the PomBase ontology term page documentation and the GO documentation on the GO graph and Relations in GO for more information.)
- GO Slim terms applicable to the gene.
- GO annotations may have extensions to capture any of several types of additional detail. S. pombe genes link to PomBase gene pages, and ontology term names link to ontology term pages.
The detailed view shows annotations to all GO terms, and includes more details for each annotation. It shows separate entries for repeat determinations of a given gene/term/extension combination (if supported by more than one line of evidence and/or reported in more than one paper), and annotations to terms hidden in the summary view:
The unique ID and name for a GO term, linked to an ontology term page as described above.
An abbreviation (code) for the type of (see “Evidence codes” below) that supports the annotation. The evidence categories come from the set of evidence codes defined by the GO Consortium.
An additional ontology term or identifier that provides supporting details for annotations using certain evidence codes (see below and GO documentation).
An optional qualifier that modifies the connection between the gene product and the GO term. Entries come from the set of allowed qualifiers described in GO’s annotation overview or internal PomBase usage.
The paper from which the annotation comes.
The number of genes annotated to the term, linked to an ontology term page as described above.
GO Slim terms applicable to the gene.
GO annotations may have extensions(see “Annotation extensions” below) to capture any of several types of additional detail. S. pombe genes link to PomBase gene pages. Protein Ontology (PRO) terms, which identify specific processed or modified forms of a protein, can be used in extensions or to indicate which form is active; both are displayed here.
Term ID and name
Annotations are made to the definition of a term, not the term name itself, so we recommend that users always read the term definition. The definition is critical because an ontology term name may change over time, but if the meaning of a definition changes the term must be obsoleted, and the associated genes must be reannotated to the correct definition. This procedure makes ontologies very robust to changes in biological knowledge, because if the definition is constant terms can be repositioned in the ontology (i.e. parents terms can be added or removed) without affecting the validity of the annotations that are attached to it.
The definition of a term can be found on the ontology term page linked to the term name and ID.
GO Structure
GO is structured in a hierarchal order with less specific terms being parents of more specific child terms. A child term may have multiple parents and multiple children; the BP mitotic sister chromatid segregation, for instance, has child terms representing each part of the segregation process (sister chromatid cohesion, separation, etc.) as well as parent terms connecting it to both the mitotic cell cycle and chromosome segregation. Crucially, whenever an annotation is made to a term, the gene product is automatically annotated to all the parent terms. The ancestry of a term can be viewed in browsers such as AmiGO or QuickGO, accessible via links on the ontology term page. For more information, see the GO graph documentation.
Multiple relationships exist to describe the links within the ontologies. A child term can have an is_a relation to the parent term, where the child is a more specific type of the parent, or a part_of relationship where the child makes up a part of the parent. For instance, the mitochondrion is_a intracellular organelle and is part_of a cell. Additionally, GO also include regulatory relationships. For more information on relationships in GO, see the Relations in GO documentation.
Evidence codes
In PomBase, every annotation is supported by a reference that states where the annotation comes from, and an evidence code that describes the type of data that supports the annotation. An annotation may be inferred from experimental ‘wet lab’ data, backed by a literature reference and citing experimental evidence such as IDA (Inferred from Direct Assay) or IMP (Inferred from Mutant Phenotype). Further information on evidence codes is available in the GO Evidence Codes documentation.
Another source of annotations come from computational methods. Please note that all computational annotations are based on predictions. In cases where a sequence model has been used to annotate genes, but the genes annotated based on the model have not been manually checked, the IEA (Inferred from Electronic Annotation) evidence code is assigned. If the annotations have been manually checked other evidence codes may be used, for instance ISO (Inferred from Sequence Orthology) or ISM (Inferred from Sequence Model). PomBase uses ISO to cross-reference to the roles of known S. cerevisiae genes, and uses ISM when domains present in a gene product can give clues to its biological role.
For some types of evidence, such as sequence comparisons or interaction data, it is important to note what gene or gene product was used in the comparison or detected in the interaction. In these cases the With/From column provides more information regarding the source of the information.
Annotation extensions
Where available, annotation extensions are displayed underneath the GO term name. The extensions provide additional specificity to the annotation by linking the term to another ontology term or a gene product via a relationship. Examples include specifying substrates of molecular functions or specifying the cellular localization during a process (for instance, S. pombe pka1 has protein serine/threonine kinase activity and has the substrates mei3 and rst2. It is a cellular component of the nucleus during nitrogen starvation, but found in the vacuole during glucose starvation).
The GO Consortium provides further information on annotation extensions in its file format guide, on a wiki page, and in publications from 2014 and 2017. PomBase converts many extension names to more human-friendly text, as described here.
If an extension mentions another S. pombe gene, the extension data will also be displayed as an annotation in the “Target of” section of the page for that gene.
PRO terms can be used in extensions, and PRO terms that are used to associate a GO annotation with a specific modified or processed form are also listed with annotation extensions. In both cases, PRO IDs link to Protein Ontology web pages. Note that PomBase uses human-friendly display names that differ from the full names on the PRO pages; abbreviations used in the display names are included in the extension display documentation.
Finding other genes annotated to a specific GO term
From a gene page, all S. pombe genes annotated to a term (or its children) can be found by clicking on a term name or ID to reach the ontology term page.
Additionally, the advanced search can be used to search for all genes annotated to a particular GO term (see the advanced search documentation for more information). To find annotations to specific GO terms in organisms other than S. pombe we recommend using AmiGO or QuickGO.
Gene page: Gene structure history
The “Gene structure history” section in the gene page shows all previous gene structures for the main feature of a gene (CDS for coding genes, and transcript for RNA genes). If available, the reasons for the change are indicated as comments or references to databases such as PubMed. In addition, a link to the annotated genome sequence before the structure was changed is provided.
List of all gene structure changes
You can find a list of all changes to all gene structures in this file. To download the file, right-click here and select “Save link as…”. Every pair of rows in the file corresponds to a change in the gene structure. The column Before / After indicates whether the coordinates refer to the gene structure before or after the change. In addition, if a reference was added or removed, it appears on the added or removed row, respectively. Comments associated with changes are also included.
Before using these coordinates for analysis, take into account that they may refer to a previous genome sequence / assembly (nucleotide sequence may have changed). You can find a list of the dates where the genome sequence has changed in this file. The relevant columns in the file are:
- date: date of the change.
- chromosome: chromosome affected.
- link: link to the file prior to the change.
For example, to extract the sequence of SPAPB15E9.01c before 2002-03-22, complement(3980427..3982657):
- Download the sequence of chromosome 1 prior to that change (the one where revision is 20011004). https://www.pombase.org/data/genome_sequence_and_features/artemis_files/OLD/20011004/chromosome1.contig
- Extract the feature from that genome sequence.
Gene page: Literature
The Literature section of a gene page lists the papers that have curated data for the gene or its product.
At the top of the section, there is a link to search PubMed for any papers on the gene. This may retrieve papers not on the gene page Literature list, if there are papers not yet curated (or spurious matches to the search criteria).
For each paper, the full citation and the number of genes curated from the paper are shown, and a “Details” link goes to the publication page.
By default, the list is sorted alphabetically by first author. Use the “Sort by” links to change the order.
Gene page: Modifications
The Modifications section lists protein modifications that have been manually curated, using terms from the PSI-MOD ontology, for protein-coding genes. PomBase will add RNA modifications to this section in the future, when relevant data are curated.
Ontology Annotations for Protein Features
The summary view shows only the names of the most specific terms used to annotate the gene:
The detailed view shows more information for each annotation, and may display additional terms:
- Name and ID of the ontology term
- Modification annotations may have extensions (see below) to capture any of several types of additional detail. S. pombe genes link to PomBase gene pages, and GO term names link to PomBase ontology term summary pages.
- The summary view is filtered, using the ontology structure, so that it shows only the most specific terms used to annotate a gene. Modification annotations curated for a gene using less specific terms (“superclasses” or “ancestors” in the ontology) appear only in the detailed view.
- An abbreviation (code) or brief description for the type of evidence that supports the annotation. Modification annotations use some of the codes defined by the GO Consortium, plus a small subset of the Evidence Ontology (ECO).
- The residue(s) modified (where available). Note: for histones, residue numbering assumes that the initiator methionine is removed.
- The published source of the annotation (where available)
- The total number of genes annotated to this term or any of its descendants, linked to a list of those genes. The gene list page includes basic information about the ontology term, and a link to send the gene list to the advanced search.
Annotation extensions
Where available, annotation extensions are displayed underneath the ontology term name. The extensions provide additional specificity to the annotation, often by linking the term to another ontology term or a gene product via a relationship. Examples include specifying the gene product that adds or removes a modification, specifying modified residues, or specifying that the modification is observed during a phase or process. For example, in S. pombe Lys4 (shown above) is phosphorylated on a serine residue during M phase of the mitotic cell cycle. Likewise, S. pombe Cdc2 is phosphorylated during G2, and phosphorylated on Tyrosine 15 by Wee1; it is phosphorylated during G2 but not M phase of the mitotic cell cycle; other extensions are also available for Cdc2.
The annotation extension field can also be used to indicate modification site occupancy, for experiments that measure the proportion of copies of the protein (or RNA) that have the modification.
Note: unlike GO annotations, for modification annotations extensions are not considered for display filtering. Annotations to less specific terms are hidden in the summary view whether they have extensions or not.
Gene page: Phenotypes
PomBase defines a phenotype as an observable characteristic, or set of characteristics, of an organism that results from the interaction of its genotype with a given environment. In PomBase, phenotypes are annotated using terms from the Fission Yeast Phenotype Ontology (FYPO). FYPO uses several existing ontologies from the Open Biological and Biomedical Ontologies (OBO) collection to construct formal definitions. Basic documentation for FYPO is available at the OBO Foundry, and further information is available on the FYPO wiki).
In the phenotype annotation display on PomBase gene pages, the first item shown is a brief summary indicating whether cells with a null (deletion) allele of the gene are viable or inviable, or either depending on experimental conditions. Next, single-locus phenotypes are shown in two tables. The first table lists phenotypes observed at the population level, such as viability in culture, and the second shows cell-level phenotypes. Note that the viable/inviable population terms describe whether a gene is essential or not, and see the wiki FYPO Content and Structure documentation for more information on cell and population phenotypes. Finally, two more tables list population-level and cell-level multi-locus phenotypes, i.e. phenotypes associated with double mutants, triple mutants, etc, and the relevant genotype details. Diploid genotypes are included in the single- or multi-locus tables as appropriate.
Each table includes ontology term details and supporting data. The summary view shows just the essentials: The list of terms is filtered, using the ontology structure, so that it shows only the most specific terms used to annotate a genotype, and each unique combination of gene, FYPO term, allele(s) and extension(s) is shown once. For single-allele phenotypes, the display includes:
- The FYPO term name, which links to a page with additional information, including the term definition, any synonyms, relationships to other FYPO terms, and annotations to the term or its descendants. (See the ontology term page documentation for more.)
- Allele details, including a name (if one is used in the literature) and description (where known). Diploid genotypes specify both alleles for the locus, and are shown in bold. Mouse over the allele name to show the allele type, which indicates whether partial deletions or altered residues refer to amino acids or nucleotides, and expression level. If you can provide a description for any allele shown as “unknown”, please contact the PomBase curators.
- Phenotype annotations may have extensions to capture penetrance (proportion of a population that shows the phenotype) or severity (previously designated “expressivity”), or to document which gene or protein used in an assay for level, localisation, etc. S. pombe genes link to PomBase gene pages. Severity and penetrance use the relations has_severity and has_penetrance respectively, and can have values such as “high”, “medium”, or “low”. Penetrance can also use numerical values. A gene or gene product used in an assay is stored using the appropriate PomBase systematic ID and the relation assayed_using; the relation is converted to affecting in the gene page display. If a mutation affects an activity that modifies another gene product, extensions may capture the affected enzyme, the affected substrate, or both. The relation assayed_enzyme is displayed as affecting activity of on gene pages, and assayed_substrate is shown as affecting substrate.
- The phenotype display can be filtered to show subsets of the total set of annotations. Two filters, for ploidy and ontology terms, are available in the summary or detailed view. If there are both haploid and diploid genotypes curated, the first filter defaults to “Haploid or Diploid” to show all genotypes. The term filter lists several broad phenotypic categories derived from high-level FYPO terms:
Choose one to restrict the annotation display to terms in the selected branch of FYPO. When term filtering is active, a message appears to indicate that not all annotations are shown:
Change the selection back to “No filter” to see annotations to all terms.
The detailed single-locus phenotype view shows annotations to all FYPO terms, and includes more details for each annotation. It shows separate entries for repeat determinations of a given gene/term/allele/extension combination (if supported by more than one line of evidence and/or reported in more than one paper), and annotations to terms hidden in the summary view:
The unique ID and name for a term in the phenotype ontology. The ID links to a page with additional information, including the term definition, any synonyms, relationships to other FYPO terms, and annotations to the term or its descendants. (See the ontology term page documentation for more.)
Allele details, including a name (if one is used in the literature) and description (where known). The column is headed “Genotypes” for consistency between the single- and multi-locus displays. Diploid genotypes specify both alleles for the locus, and are shown in bold. Each genotype name links to a page with full details (type, description, and expression) for its allele(s), links to gene pages, and a list of all phenotype annotations for the genotype. If you can provide a description for any allele shown as “unknown”, please contact the PomBase curators.
Mouse over the allele name to show the allele type, which indicates whether partial deletions or altered residues refer to amino acids or nucleotides, and expression level.
The phenotype display can be filtered to show subsets of the total set of annotations. The ploidy filter (not shown in this screenshot) selects haploid, diploid, or both genotypes where curated. The term filter, available in the summary or detailed view, lists several broad phenotypic categories derived from high-level FYPO terms. Choose one to restrict the annotation display to terms in the selected branch of FYPO. Change the selection back to “No filter” to see annotations to all terms. In the detailed view, annotations can also be filtered by evidence or throughput by choosing an descriptions from pulldown menus. Change the selection back to “No filter” to see annotations using any evidence type. Different filters, such as term and evidence, can be combined (note that some term/evidence combinations have no matching annotations). When any filtering is active, a message appears to indicate that not all annotations are shown.
A brief descriptor for the type of evidence that supports the annotation. The evidence categories come from the Evidence Ontology (ECO).
Information about experimental conditions, such as temperature, type of medium used, etc. Descriptions come from a small ontology maintained by PomBase curators.
The paper from which the annotation comes.
Phenotype annotations may have extensions to capture penetrance (proportion of a population that shows the phenotype) or severity (previously designated “expressivity”), or to document which gene or protein used in an assay for level, localisation, etc. S. pombe genes link to PomBase gene pages. Severity and penetrance use the relations has_severity and has_penetrance respectively, and can have values such as “high”, “medium”, or “low”. Penetrance can also use numerical values. A gene or gene product used in an assay is stored using the appropriate PomBase systematic ID and the relation assayed_using; the relation is converted to affecting in the gene page display. If a mutation affects an activity that modifies another gene product, extensions may capture the affected enzyme, the affected substrate, or both. The relation assayed_enzyme is displayed as affecting activity of on gene pages, and assayed_substrate is shown as affecting substrate.
Similar displays are used for multi-locus phenotypes. Unless otherwise noted below, all items are as described above for single-locus phenotype displays.
The multi-locus summary shows FYPO terms and genotype descriptions:
- The FYPO term name, which links to the page for the term.
- Genotype details, including a name (if one is used in the literature) and descriptions for the relevant alleles (where known). Mouse over any genotype name to show more allele details, or click to go to the genotype detail page. Multiple genotypes annotated to the same term are separated by commas. Diploid genotypes specify both alleles for each locus, and are shown in bold.
- Display filters for ploidy and FYPO terms (as described above for single-locus phenotypes).
The detailed view includes:
- The unique ID and name for a term in the phenotype ontology, with links to the FYPO term page.
- Genotype details, including a name (if one is used in the literature) and descriptions for the relevant alleles (where known). Mouse over any genotype name to show more allele details, or click to go to the genotype detail page. Multiple genotypes annotated to the same term are listed one per line. Diploid genotypes specify both alleles for each locus, and are shown in bold.
- Display filter for ploidy, FYPO terms, evidence, and throughput (see above).
- Evidence description (see above).
- Experimental conditions (see above).
- The paper from which the annotation comes.
Annotation extensions are also included in the multi-locus Summary and Full views (although none are included for the annotations in the above illustrations), using the same display as for single-locus phenotypes.
Also see the Advanced search documentation for information on finding genes annotated to phenotype terms.
Gene page: Protein features
Gene pages for protein-coding genes have a section describing protein features. Also see the Modifications documentation.
- The graphical view is interactive, and shows the positions of domains and other features. Mouse over any feature to highlight its entry in the table, and to see a pop-up with the feature ID, name, nad position.
- The table of protein families and domains is described in more detail below.
- This section provides manual curation that ensures that large protein families (e.g. the WD family) include all known members. These manual annotations are provided because many families in protein family databases are rebuilt during the release cycle to include new sequences, and as a result gene products are sometimes lost or gained from protein families, and false negatives are common. This section is also used to capture published subfamily members which may be collected into a single family in protein family databases.
- Any motifs or features annotated using Sequence Ontology (SO) terms.
- Table of the protein’s physical properties
Protein Families and Domains
- Feature ID of this family or domain in the originating database. Where feasible, the ID links to the source database. Databases include Pfam, SMART, Prosite, Gene3D, SUPERFAMILY, TMHMM and Panther.
- Source database name
- Name of the matching feature in the contributing database
- ID of the InterPro entry that includes the feature. InterPro classifies proteins into families using predictive models provided by several different databases that make up the InterPro consortium. InterPro is useful for assessing the species distribution of a particular family or domains.
- The description of the domain in InterPro, from the contributing database
- Start and end coordinates, showing the location of the feature within the protein
- Link to a list of other fission yeast proteins which are members of the family or have the domain
- Link to the InterPro entry for the feature
- Link to the Pfam entry for the protein, which shows domain organization
- Transmembrane domain coordinates, where applicable
Note that some of the listed features (e.g. transmembrane domains from TMHMM) are predictions. Consult the contributing databases for further information, or contact the PomBase curators if you notice any problems with annotated or predicted features.
Gene page: Sequence
The Sequence section of a gene page provides a widget to download DNA sequences for any gene, and amino acid sequences for protein-coding genes, as well as links to send sequences to BLAST. For protein-coding genes, the predicted amino acid sequence is displayed by default:
If two or more transcripts are annotated for a gene, the primary transcript is shown by default. Use the selector to switch between transcript isoforms.
Toggle to show the amino acid sequence for protein-coding genes (not available for non-coding RNA genes, which always show nucleotide sequence).
Button to save the displayed sequence to a file, with the following options:
- Displayed Sequence as FASTA
- Genome region as GenBank: This feature downloads the genome region, in GenBank format. The file always includes the introns, exons and UTRs. You can include extra upstream or downstream sequences, if the “Show nucleotide sequence” is toggled but other settings are ignored. Files can be opened in sequence viewers (Snapgene, Ape, Benchling…) and contain the sequence feature annotations (CDS with labelled introns, translated sequence, UTRs, etc.).
- Genome region as EMBL: Same as previous one, but in EMBL format.
Links to send the displayed sequence to BLAST at NCBI or Ensembl.
The peptide sequence header shows the transcript ID and the protein length.
For non-coding RNA genes, and for protein-coding genes with “Show nucleotide sequence” selected, more options are available:
Transcript selector (as above)
Toggle to show the amino acid sequence (not available for non-coding RNA genes).
Controls to add UTRs, introns, or flanking sequences to the displayed sequence. For upstream or downstream sequence, use the up/down control to increment by one base, or type or paste a number in the box.
Link to save the displayed sequence to a file.
Links to send the displayed sequence to BLAST at NCBI or Ensembl. DNA sequences link to BLASTN by default.
The nucleotide sequence header shows the transcript ID and indicates what is included.
When the “Show translation” option is selected, irrelevant controls are hidden and BLASTP links are shown:
Gene page: Target of
The “Target of” section describes genes that affect the gene of interest. Genes listed under “Target of” may include upstream regulators or enzymes that modify the product of the gene of interest. For example, the “Target of” annotations for S. pombe cdc2 indicate that it is a substrate of, and regulated by, the kinase Wee1 and the phosphatase Cdc25 (among others).
Target of data are derived by taking the reciprocal of ontology annotation extensions (using GO annotation extensions and phenotype annotation extensions). The table includes:
- Ontology: GO or FYPO, i.e. the ontology in which the annotation was made
- Relationship: indicates how the genes are connected. The relationship is the reciprocal of the relation used in the originating annotation extension, as noted in the Annotation extension relation display documentation.
- Gene: the gene whose product affects the gene of interest.
- Product: the targeting gene’s product description.
- Reference (hidden in “summary” view): the source of the annotation.
Gene page: Transcript
The Transcript section of a gene page shows the positions of introns and exons in each transcript. The default is a graphical view:
The default view shows one diagram per annotated transcript, with intron and exon positions hidden. Click “Show exon/intron/UTR positions” to display a table under each transcript diagram:
ID(s) and genomic location(s). The transcript systematic ID is the gene systematic ID with a suffix appended. The primary transcript suffix is “.1”, and any additional annotated transcript isoforms receive sequentially numbered suffixes.
By default, intron and exon positions are shown in the table as genomic coordinates. When the “Show transcript coordinates” button is checked, positions in the table are numbered using the annotated transcription start site as 1.
Mouse over any exon or intron to highlight its coordinates in the table, and bring up a box with position details. Genomic coordinates and within-transcript positions appear in the pop-up no matter which is selected in the main display.
Mouse over any entry in the exon/intron tables to show the box with position details.
Genetic and physical interactions
The Interactions section of a gene page displays genetic and physical interactions for a gene (or its product), in BioGRID format. All interactions are curated manually by PomBase or BioGRID curators.
Each table has five columns:
The first column (with no header) describes the interaction. The text reflects the type of evidence listed in the Evidence column and, where applicable, the directionality of the interaction.
Interacting gene: The gene that interacts with the gene of interest, linked to its gene page
Interacting product: The description of the interacting gene’s product, from its gene page
Evidence: The type of genetic interaction observed, or the type of experiment performed to detect a physical interaction. The evidence categories come from BioGRID, and are described on their Experimental Evidence Codes documentation page.
Reference: The paper cited to support the interaction
Additional fields for Genetic Interactions
Since November 2022, new or updated Genetic Interaction annotations are linked to phenotype annotations and alleles. We continue to display interactions in the old format by default (showing only genes and interaction type), but if you expand the annotation, you can view the associated genotypes and phenotypes.
More on Genetic Interactions
The definitions of all genetic interactions can be found in the BioGRID wiki. It is worth reading these definitions, as the language often used in publications does not match the naming of genetic interactions. For example, in publications we can find “double deletion of gene X and Y rescues the defects cellular morphology caused by deletion of gene Y”. However, for BioGRID this is a phenotypic suppression not a rescue, since rescue is reserved for lethality or growth defect. The genetic interactions that are used in low throughput curation in PomBase are:
- Dosage Growth Defect: Overexpression/increased dosage of one gene causes a growth defect in a strain that is mutated/deleted for another.
- Dosage Lethality: Overexpression/increased dosage of one gene causes lethality in a strain that is mutated/deleted for another gene.
- Dosage Rescue: Overexpression/increased dosage of one gene rescues the lethality or growth defect of a strain mutated/deleted for another gene.
- Phenotypic Enhancement: Mutation/deletion/overexpression of one genes results in enhancement of any phenotype (other than lethality/growth defect) associated with mutation/deletion/overexpression of another gene.
- Phenotypic Suppression: Mutation/deletion/overexpression of one gene results in suppression of any phenotype (other than lethality/growth defect) associated with mutation/deletion/overexpression of another gene.
- Synthetic Growth Defect: Mutations/deletions in separate genes, each of which alone causes a minimal phenotype, but when combined in the same cell results in a significant growth defect under a given condition.
- Synthetic Lethality: Mutations/deletions in separate genes, each of which alone causes a minimal phenotype, but when combined in the same cell results in lethality under a given condition.
- Synthetic Rescue: Mutation/deletion of one gene rescues the lethality or growth defect of a strain mutated/deleted for another gene.
In addition, we curate the following types of genetic interaction not covered by BioGrid.
- Synthetic Phenotype: Mutation/deletion/overexpression in separate genes produces a phenotype that is not present in either of the single mutations/deletions/overexpressions under a given condition.
When exporting the data to BioGrid, “Synthetic Phenotype” genetic interactions are exported as “Phenotypic Enhancement”, see this GitHub issue for details.
Below is a decision making tree to determine the type of genetic interaction from the phenotypes of the single and double mutant. “Interacting allele” refers to the allele that is not present in the single mutant:
Genotype pages
Genotype pages are analogous to gene pages, but describe the alleles that make up a genotype, and show phenotypes associated with the genotype.
The genotype name. A short and/or memorable name can be assigned, but otherwise the default name is constructed by concatenating the names of the alleles that make up the genotype.
Each genotype in composed of one or more alleles. The table lists details for each allele of interest in the genotype. Any curated background details will be shown above the table of alleles.
- Gene name, linked to its gene page
- Allele name and description. For point mutations and partial deletions, the description specifies the positions, and indicates altered residues for point mutations.
- The allele type specifies what kind of change the allele description represents, e.g. amino acid mutation, deletion, other.
- The expression level indicates the amount of gene product present in the assayed cells, or “Not assayed or wild type” if the level was not directly measured.
Phenotypes annotated to the genotype are displayed as described in the gene page documentation.
For diploid genotypes, the table of details includes both alleles of each locus:
The Locus column contains the gene name, linked to its gene page, and spans two rows, one for each allele at the locus. Allele details are as described for haploid genotypes.
Getting started
Getting started in the Schizosaccharomyces pombe community
To get started as a new community member, you can:
- Join the pombe mailing list with more than 1300 subscribers, where you can ask and answer questions about fission yeast generally, get notifications about PomBase updates and get invitations to the monthly online seminar PombeTalks. Join here.
- Join the pombe Slack channel, to get in touch with other fellow Schizosaccharomyces pombe researchers. See the instructions to join here. If this is your first time using Slack, you can get started with this guide.
- Read the basics about Schizosaccharomyces pombe biology and experimental methods in the Forsburg Lab website.
- Read about the history and importance of Schizosaccharomyces pombe as a model system PMC4896181 and a primer introducing genetic and bioinformatic tools: PMC4596657
For PomBase help you can read our Frequently Asked Questions or send us an email at helpdesk@pombase.org.
If you use Pombase for your research, please cite or acknowledge the resource in your publications. This is extremely important to indicate the importance of resources to funders. How to cite PomBase.
Types of pages in PomBase
PomBase is centred around Gene Pages so this is a good place to begin to familiarise yourself with how data is organised. You should visit your favourite gene page, but for this example we are using pol1, the DNA polymerase alpha catalytic subunit. You can access the page by typing the gene name (i.e. pol1) into the search box at the top-right of the website, or at this link.
At the top of the page, you will find some basic information about the locus and gene product. Immediately below is a view of the genomic context of the gene in the JBrowse genome browser. (documentation to access browser data tracks is here):
Read more about the names of genes…
The same gene may be known by different names. In PomBase, we consider three types:
- Systematic ID, a unique identifier that represents exclusively this gene in Schizosaccharomyces pombe.
- Gene standard name, the most commonly used name of this gene, that may not be exclusive to pombe, and could even be used as a synonym of other fission yeast genes. This name will frequently be the same as the orthologous gene in S. cerevisiae, (the ortholog of pol1 in S. cerevisiae is also called pol1), but be aware there are many notable examples where the same name is used for different genes in other species. Some genes don’t yet have a standard name, but if you study them you can name them.
- Synonyms, alternative names for this gene that have been used in the literature before. We encourage you to use the standard name in publications where possible.
On the left side of the Gene Page, there is a menu listing the sections in the page (GO molecular function, GO biological process, etc.). Each section contains different kinds of annotations. Go through them and click on the 
button to see what information is displayed in each section. Most sections show a “summary view” of the experimentally relevant information so that it is easier to consume the biological context. The “Show details” link uncollapses the section to show important associated information such as evidence and provenance, often presenting multiple sources supporting the same annotation. You also will notice that many of the displayed annotations are blue and link to other types of pages:
GO term pages: contain the definition of the GO term and lists all the genes annotated to a specific GO term and its “child” terms.
Read more…
- GO annotations link a gene to a GO term that describes the molecular function(s) of its gene products, the process(es) they are involved in their localisation in the cell or their presence in macromolecular complexes.
- A term name may change over time, but if the meaning of a definition changes the term must be obsoleted, and the associated genes reannotated to the correct definition. This makes the term definition critical and curators must always ensure that the definition is appropriate for the annotation.
- A GO term can be linked to several parent terms through relationships. Let’s take the term GO:0001055 (RNA polymerase II activity), graph below.
- RNA polymerase II activity is a GO molecular function.
- This activity is a specific type of GO:0003899 (DNA-directed 5’-3’ RNA polymerase activity), so GO:0001055 is linked to GO:0003899 through an is_a relationship.
- This activity is part of the GO biological process GO:0006366 (Transcription by RNA polymerase II), so GO:0001055 is linked to GO:0006366 through a part_of relationship.
- This activity occurs at the GO cellular component GO:0000785 (chromatin) so GO:0001055 is linked to GO:0000785 through a occurs_in relationship.
- In PomBase GO term pages, for simplicity we do not present inter-ontology links and only link to children and parent terms of the same ‘aspect’ (i.e molecular function, biological process, cellular component) these include terms related to each other by the relationships is_a, part_of and the 3 ‘regulates’ relationships. For instance, in the page of GO molecular function GO:0003899 (DNA-directed 5’-3’ RNA polymerase activity):
- We include GO:0001055 (RNA polymerase II activity), which is also a GO molecular function, linked to GO:0003899 through an is_a relationship
- We do not include the cellular component GO:0000428, linked to the molecular function GO:0003899 through a capable_of relationship.
- If you expand a term by clicking on the ‘+’ icon on its left, you can see the relationship to the term in the current page.
- Learn more about GO, its development and use in analyses in this webinar by former PomBase curator Antonia Lock.
Phenotype pages the Fission Yeast Phenotype Ontology (FYPO) term pages: provide the phenotype definition and list all the genotypes annotated to a FYPO term and its ‘child’ terms, as well as link to the parent terms. Read more…
Read more…
- As for GO, the simplest relationship between FYPO terms is is_a, in which the child term describes a more specific phenotype than the parent. For example, FYPO:0006885 (decreased protein level at mitotic spindle) is_a FYPO:0001324 (decreased protein level during vegetative growth), which in turn is_a FYPO:0001325 (altered protein level during vegetative growth).
- Other relationships also exist, such as output_of, which links a given phenotype to another that causes it. For example, FYPO:0000118 (multiseptate vegetative cell) is output_of FYPO:0000032 (abnormal cytokinesis). Therefore, in the page of FYPO:0000032, the annotations of FYPO:0000118 are also displayed.
- Read more about FYPO, our phenotype ontology here.
Genotype pages: contain all the phenotypes associated with a genotype as well as the alleles that constitute that genotype. Example: mal3delta.
Other ontology term pages. Read more
Advanced search / query builder
You can query PomBase annotations using a Graphical User Interface, the “Advanced search” (https://www.pombase.org/query). You can make lists of genes that satisfy a certain condition, and perform operations with these lists. Below some examples:
Disease-associated genes that give a cytoskeleton phenotype in Schizosaccharomyces pombe:
Read how to make this query…
- Get the list of all disease-associated genes:
- Click on Commonly used queries > All disease associated genes.
- Get the list of all genes annotated with a cytoskeleton phenotype:
- Click on Phenotype
- Type “abnormal cytoskeleton” and select FYPO:0002397.
- Click on Submit
- You should see two queries in the Combine queries table below named “genes annotated with”abnormal cytoskeleton” […]” and ”All disease associated genes”. Select both by clicking on the tickbox on the left.
- Then click on intersect / and. This will generate an intersection of both lists (genes present in both) with genes that satisfies both conditions.
- The number in the “Results” column is the number of genes that satisfy those conditions. Click on it to see the lists of genes.
- In that page, you can choose the columns to be displayed, and export your data for further usage.
- Get the list of all disease-associated genes:
Genes that locate to the Golgi apparatus or the endoplasmic reticulum and cause an exocytosis or endocytosis phenotype.
Read how to make this query…
- Get the list of all genes that have annotations saying that one of their gene products locates to the Golgi apparatus (they are annotated to GO:0005794, “Golgi apparatus”):
- Click on GO
- Type “Golgi apparatus” and select GO:0005794.
- Click on Submit
- Get the list of all genes that have annotations saying that one of their gene products locates to the endoplasmic reticulum (they are annotated to GO:0005783, “endoplasmic reticulum”).
- Click on GO
- Type “endoplasmic reticulum” and select GO:0005783.
- Click on Submit
- In the Combine queries table below, select both genes annotated with “Golgi apparatus” and genes annotated with “endoplasmic reticulum” by clicking on the tickbox on the left.
- Then click on Union / or. This will generate a union of both lists (genes present in either of the lists) with genes that satisfy either condition.
- Get the list of all genes annotated with an exocytosis phenotype:
- Click on Phenotype
- Type “abnormal exocytosis” and select FYPO:0007873
- Click on Submit
- Get the list of all genes annotated with an endocytosis phenotype:
- Click on Phenotype
- Type “abnormal endocytosis” and select FYPO:0003886
- Click on Submit
- Do a union of the phenotype lists, as for the GO terms.
- Still in the Combine queries table, select both union lists, and click on intersect / and. This will generate an intersection of both lists (genes present in both) with genes that satisfies both conditions.
- The number in the “Results” column is the number of genes that satisfy those conditions. Click on it to see the lists of genes.
- In that page, you can choose the columns to be displayed, and export your data for further usage.
- Get the list of all genes that have annotations saying that one of their gene products locates to the Golgi apparatus (they are annotated to GO:0005794, “Golgi apparatus”):
Full documentation of advanced search can be found here.
Other useful links
High Confidence Physical Interaction Network (HCPIN)
The PomBase High Confidence Physical Interaction Network (HCPIN) is a collection of physical interaction data based on three subsets of Gene Ontology (GO) annotations:
- Manually curated protein binding annotations. PomBase curators annotate genes to the GO “protein binding” molecular function term (GO:0005515) when proteins are shown experimentally to interact in a pairwise, and presumably direct, manner, often by more than one method
- Targets or substrates of biochemical activity (e.g. protein kinases or phosphatases, protein methyltransferases, ubiquitin-protein ligases). When one protein is shown experimentally to modify another, a GO molecular function annotation represents the activity, and the target(s) can be captured using annotation extensions. For example, Cdc2 phosphorylates Cut3, so it is annotated to ‘protein serine/threonine kinase activity’ with the extension ‘has substrate cut3’.
- GO protein complex annotations. The HCPIN set includes both annotations supported directly by fission yeast experiments and those inferred from an experimentally characterised ortholog.
The data can be downloaded in tab-delimited format from the Download Datasets page.
Identifier mapper
The identifier mapper retrieves S. pombe gene systematic IDs and standard names for a selection of different input ID types:
- Find S. pombe genes using UniProt accessions
- Retrieve manually curated orthologs for
- S. cerevisiae: Use standard gene names (CDC28, ACT1, etc.), ORF names (YPR121W, YPL258C, etc.), or SGD IDs (SGD:S000004494, SGD:S000004635, etc.)
- Human: use standard gene names (CDK1, BRCA2, etc.) or HGNC identifiers (e.g. HGNC:1722)
- S. japonicus: use standard gene names (cdc11, pka1, etc.) or systematic IDs (e.g. SJAG_01188)
Select an input identifier type in the pulldown, and enter IDs by typing, pasting, or uploading a file:
Click “Clear” to empty the input box or “Lookup” to retrieve results.
For all query types, the number of matching S. pombe genes is shown at the top. Any unmatched IDs are shown next.
“Go back” returns to the start page, with the search settings and IDs you used filled in.
You can use the list of matching S. pombe genes in the Advanced Search “Gene names and IDs” query.
For orthology ID searches, matching S. pombe genes may fall into any of into three categories:
- one-to-one
- one-to-many
- many-to-one
- All result lists show two columns: the entered ID(s) and the matching S. pombe gene(s). Links go to PomBase gene pages. If there is a single result in the one-one or one-many section, it is displayed by default. Longer lists, and many-to-one matches, are hidden by default. Use the “Show matches/Hide matches” links to toggle the display.
For S. pombe UniProt accessions, almost all results are one-to-one; the show/hide toggle works the same as for ortholog results.
PomBase Web Site Help & Documentation
General
Gene Pages
- Basic information
- Gene Ontology
- Phenotypes
- Target of
- Transcript
- Protein features
- Modifications
- Gene expression
- Interactions
- Orthologs and paralogs
- Sequence
- Taxonomic conservation
- Disease association
- Controlled curation
- External references
- Literature
Searching
JBrowse Genome Browser
- Getting started with PomBase JBrowse - an introductory guide to browser navigation, track loading, metadata, etc. (by Antonia Lock)
- Also see the General entry in the JBrowse Help menu
- See “File Formats” below to submit data
QuiLT
- Documentation for the Quick Little Tool for gene list visualisation
Non-gene sequence features
Other PomBase Pages
- GO Slim Documentation and Usage tips
- Ontology term pages
- Publication pages
- Genotype pages
- Fission Yeast Phenotype Ontology (FYPO) page
- High Confidence Physical Interaction Network (HCPIN)
- Data versions
How to Cite PomBase
- See the Citing PomBase page
File Formats for Data Submission
PomBase accepts batch submissions of certain types of data that appear on PomBase gene pages. For these data types, we use dedicated PomBase-specific formats:
- Phenotypes
- Modifications
- Qualitative gene expression
- Quantitative gene expression
- HTP data for JBrowse tracks
For data that can be connected with sequence features or coordinates, and displayed as tracks in the genome browser, see the data format FAQ and further details linked there.
Linking to and from PomBase
Linking to PomBase: To link to any PomBase gene page, use the systematic ID for the gene in a URL with the syntax “https://www.pombase.org/gene/[systematic ID]”. For example, https://www.pombase.org/gene/SPBC11B10.09 links to the gene page for cdc2.
Linking from PomBase to external resources: We can provide links from PomBase gene pages to gene- or gene product-specific S. pombe data for any resource that uses URLs with PomBase systematic IDs. Please contact the PomBase Curators for more information.
Comparative Genomics
We plan to add specific documentation about comparative genomics using S. pombe here. In the meantime, you can look at the documentation for Ensembl Compara.
More information …
For help with anything in PomBase not covered here, you can contact the curators.
Miscellaneous sequence features
View sequence features in Artemis
Sequence features can also downloaded from data directory and viewed in Artemis. See this FAQ for more information.
Centromeres
Modification data bulk upload format
PomBase welcomes submissions of published large-scale modification data sets. We have devised a tab-delimited text file format for bulk modification data.
Include a header line that labels the columns – use the entry in the Contents column below as the column header text.
| Column | Contents | Example | Mandatory? | Multiple entries allowed? |
|---|---|---|---|---|
| 1 | Gene systematic ID | SPBC11B10.09 | Yes | No |
| 2 | Gene name | cdc2 | No | No |
| 3 | Ontology ID | MOD:0000001 | Yes | No |
| 4 | Evidence | ECO:0000006 | Yes | No |
| 5 | Residue | S72 | No | Yes |
| 6 | Extension | added_by(PomBase:SPBC11B10.09) | No | Yes |
| 7 | Reference | PMID:24763107 | Yes | No |
| 8 | Taxon | 4896 | Yes | No |
| 9 | Date | 2014-05-01 | Yes | No |
Notes:
At present we accept protein modification data, using PSI-MOD IDs in the Ontology ID column. We plan to accept RNA modification data in the future. More information is available in the gene page modifications documentation.
Use one line per modified position (multiple entries are allowed only in the Extension column).
File columns:
- Include the systematic ID for each gene. You can look up systematic IDs on gene pages, or refer to the file of all gene names from the dataset download page.
- Gene names are optional. If you include them, use standard names in column 2 (see gene pages or the file of all gene names from the dataset download page.
- For help finding suitable ontology (PSI-MOD) terms to describe your phenotypes, see the Canto protein modification documentation. If you can’t find a term you need, email the helpdesk for assistance; we can advise you, and request new terms as needed.
- For the Evidence column, we use a small selection from the Evidence Ontology (ECO). You are welcome to enquire with us in advance to find out which ECO terms/IDs fit your experiments, but we can accept files with brief descriptions, which curators will convert to ECO IDs.
- The Residue column indicates the position modified. For protein modifications, use one-letter amino acid code. Multiple entries are allowed, but only for cases where two or more of the same modification are known to be present at the same time. Separate entries with commas (e.g. S72,T85). Position numbering should reflect the current sequence data in PomBase. Please refer to the Gene Coordinate Changes page to ensure that your residue position entries are up to date. Also note that histones are conventionally numbered assuming the initiator methionine is removed (i.e. every position in the mature protein is numbered, and is 1 less than the apparent numbering predicted by translating the ORF).
- See the table below for allowed annotation extensions. Multiple extensions can be included for a modification. Separate extensions with a comma (,) if they combine to form a “compound” extension (all parts apply together), or with a pipe (|) if they are independent. You can also use separate rows for annotations with independent extensions.
- The Reference column has the publication’s PubMed ID (PMID).
- The taxon will usually be 4896 (the NCBI taxon ID for Schizosaccharomyces pombe), although if you have an NCBI taxon ID for a specific S. pombe strain you are welcome to use it
- The date is the date on which the annotations are created; you may use the paper publication date or the date on which you prepare your data file. Format: YYYY-MM-DD
Allowed annotation extensions:
Annotation extensions can be used to provide additional information, such as a gene whose product adds or removes a modification, a process or cell cycle phase during which a modification is present, or modification site occupancy (see the gene page modifications documentation for more information). Each annotation extension consists of a relation and either an identifier or a number.
| Extension relation | Meaning | Example |
|---|---|---|
| added_by | identifies a gene product that adds the modification | added_by(PomBase:SPBC11B10.09) |
| affected_by | identifies a gene product that has some influence on the modification, but has not been conclusively shown to add or remove it | affected_by(PomBase:SPBC11B10.09) |
| removed_by | identifies a gene product that removes the modification | added_by(PomBase:SPAC24H6.05) |
| added_during | identifies a biological process or cell cycle phase during which the modification is actively added | added_by(GO:0000085) |
| removed_during | identifies a biological process or cell cycle phase during which the modification is removed | removed_by(GO:0000087) |
| present_during | identifies a biological process or cell cycle phase during which the modification is observed (note that the modification may have been added during this process – if this is known use the added_during relation – or during a preceding process) | present_during(GO:0000085) |
| absent_during | identifies a biological process or cell cycle phase during which the modification is not observed (note that the modification may have been removed during this process – if this is known use the removed_during relation – or during a preceding process) | absent_during(GO:0000087) |
| decreased_in_presence_of | use when the modification is observed at a lower level in the presence than in the absence of an extraneous substance | decreased_in_presence_of(CHEBI:84327) |
| increased_in_presence_of | use when the modification is observed at a higher level in the presence than in the absence of an extraneous substance | increased_in_presence_of(CHEBI:84327) |
| required_for | indicates that a modification is required for a GO function or process | required_for(GO:0000086) |
| occupancy | percent representing what proportion of copies of the protein have the modification | occupancy(51.5%) |
| level_fluctuates_during | identifies a biological process (e.g. the cell cycle or one or more of its phases) during which the modification site occupancy is observed to vary | level_fluctuates_during(GO:0000278) |
| multiplicity | number of modified sites detected within the same peptide fragment (relevant to mass spec. methods) | multiplicity(2) |
| in_absence_of | This relation is used to indicate attenuation of the activity of a specific gene product (either by deletion or inactivation). This extension must be used with an additional extension describing the modification | in_absence_of(PomBase:SPBC11B10.09) |
| decreased_during | identifies a biological process or cell cycle phase during which the modification is actively increased | decreased_during(GO:0034605) |
| increased_during | identifies a biological process or cell cycle phase during which the modification is actively deceased | increased_during(GO:0034605) |
Please contact the PomBase curators if you have any questions about what to use for modification IDs, Evidence, annotation extensions, or anything else you need to represent your data in this format.
Peptide motif search
The peptide motif search finds short peptide sequence matches in the predicted amino acid sequences of S. pombe proteins.
Type or paste a motif using the single-letter amino acid code. As you type, matches will appear. The results table shows each matching sequence in the context of a longer stretch of the protein sequence. The list of genes with one or more matches can be sent to the advanced search.
The search can also use wildcards, codes for groups of amino acids (e.g. any charged amino acid), and syntax to specify motifs at the beginning or end of a protein:
| Sequence | will find |
|---|---|
| CADR | any protein containing CADR |
| CA[DE]R | any protein containing CADR or CAER |
| CA[DE]+LQ | CA(any sequence of D and E)LQ |
| CA…R | CA(any three amino acids)R |
| CA.+R | CA(one or more amino acids)R |
| SPR. | SP.R |
| ^ME | proteins beginning with ME |
| LAA$ | proteins terminating LAA |
| ^.{{ "{1,20}MCA" }} | proteins with MCA in the first 20 amino acids |
Amino acid group codes
| AA group | Code | Amino acids |
|---|---|---|
| acidic | 0 | DE |
| alcohol | 1 | ST |
| aliphatic | 2 | AGILV |
| aromatic | 3 | FHWY |
| basic | 4 | KRH |
| charged | 5 | DEHKR |
| hydrophobic | 6 | AVILMFYW |
| hydrophilic | 7 | KRHDENQ |
| polar | 8 | CDEHKNQRST |
| small | 9 | ACDGNPSTV |
| tiny | B | AGS |
| turnlike | Z | ACDEGHKNQRST |
Examples:
- CA6AC will find CALAC and CAFAC
- CA0+LQ will find CA(any sequence of D or E)LQ
Ontology term pages
For each ontology term loaded into PomBase, a page summarizes essential details about the term, and shows any annotations to it or its descendants via is_a, part_of, and the regulates relations (the GO documentation on Ontology Structure and Ontology Relations has some useful information on this topic). For FYPO terms only, the has_part relation is also used.
The main illustrations use a GO term page. Note that not all ontology terms have all of the depicted features.
- Ontology term details. The term’s name, ID, and definition are shown.
- The term’s immediate parent(s), linked to the corresponding ontology term page(s).
- Links to external browsers are available for some ontologies. GO, FYPO and PSI-MOD terms have links to BioPortal, and GO term pages also link to AmiGO and QuickGO. SO IDs link to MISO.
- Link to a page that lists genes annotated to the term or its descendants. From the linked page, the gene list can be sent to the advanced search for use in queries.
- In the annotation summary view, the term of interest is listed first, followed by any descendant term that has direct annotations. For each term, genes (or genotypes) are listed in a compact display, with separate lines only for unique combinations of gene, term, and extension. As in the gene page summary display, most details are hidden.
As on gene pages, a more detailed annotation display is available:
- The detailed view shows one line per annotation, with separate entries for repeat determinations of a given gene/term/extension combination (if supported by more than one line of evidence and/or reported in more than one paper). The annotated gene (or genotype) is listed in the first column.
- The rest of the detailed annotation display (term name, extensions, evidence, reference, etc.) is as described in the gene page documentation for each annotation type.
- The table is organized into sections, one per descendant term, and each section includes genes annotated directly to the indicated term. An icon near each descendant term ID shows the relationship type that links the terms. For example, a meiotic spindle astral microtubule (GO:1990574) is a type of astral microtubule, and a mitotic spindle astral microtubule is part of an astral microtubule.
FYPO term pages have a few distinctive features:
- Links near the top of the page go to lists of genes and genotypes.
- The annotation display is split into single-allele and multi-allele sections, as on gene pages.
- Annotated genotypes (rather than genes) are listed for each term.
- In the detailed view, evidence filtering is available as described in the gene page documentation.
Ontology term pages are available for GO, FYPO, SO, PSI-MOD, and PomBase internal ontologies including the PBO description collection, the PomGeneEx descriptions for qualitative gene expression, and FYECO (previously known as PECO) for phenotype experimental conditions.
Ortholog curation
The “Orthologs” section of a gene page includes two subsections.
The first lists any orthologous genes in budding yeast (Saccharomyces cerevisiae) or human (Homo sapiens) that have been assessed and recorded manually, as described below, by curators. Budding yeast entries link to the Saccharomyces Genome Database (SGD), and human genes link to HGNC; the text descriptions come from these databases. For more information, including how to search the curated orthologs, see the FAQs on budding yeast and human orthologs.
The second subsection provides links to several resources that predict orthologs in all fungi or all species (PomBase does not manually curate orthologs in species other than budding yeast and human). For further information, see the FAQ on orthologs in additional species. (Note: these links also appear in the External references section.)
Manual ortholog prediction methods: The human and budding yeast orthologs are manually predicted based on a variety of sources. In some cases the consensus ortholog from the major ortholog predictors (Compara, Inparanoid, OrthoMCL) is used. Many distant orthologs have also been identified by PSI-BLAST matches; these alignments have been submitted to the Pfam protein family database. Other ortholog predictions come from experimental data demonstrating functional correspondence or involving membership of corresponding complexes. These predictions are also aligned and submitted to Pfam before inclusion. PomBase’s approach ensures that the breadth of coverage is greater than any individual prediction method, and includes many ortholog calls which are not detected by any automated method. Gradually, we will add and display supporting references for all orthology calls.
Paralogs
The Paralogs section lists any curated paralogous fission yeast genes.
Phenotype data bulk upload format
PomBase welcomes submissions of published large-scale phenotype data sets. We have devised a tab-delimited text file format for bulk phenotype data. A similar format is used for the downloadable file of single-allele phenotype data (with one more column at the start of each line to identify PomBase as the source; note that, because Database is column 1 in the downloadable file, column numbers differ by 1 between the download and upload formats).
Include a header line that labels the columns – use the entry in the Contents column below as the column header text.
| Column | Contents | Example (from S. pombe) | Mandatory? | Multiple entries allowed? |
|---|---|---|---|---|
| 1 | Gene systematic ID | SPBC11B10.09 | Yes | No |
| 2 | FYPO ID | FYPO:0000001 | Yes | No |
| 3 | Allele description | G146D | Yes | No |
| 4 | Expression | overexpression | Yes | No |
| 5 | Parental strain | 975 h+ | Yes | No |
| 6 | Background strain name | SP286 | No | No |
| 7 | Background genotype description | h+ ura4-D18 leu1-32 ade6-M210 | No | No |
| 8 | Gene name | cdc2 | No | No |
| 9 | Allele name | cdc2-1w | No | No |
| 10 | Allele synonym | wee2-1 | No | Yes |
| 11 | Allele type | amino acid mutation | Yes | No |
| 12 | Evidence | ECO:0000336 | Yes | No |
| 13 | Condition | at high temperature | Yes | Yes |
| 14 | Penetrance | 85% | No | No |
| 15 | Severity | medium | No | No |
| 16 | Extension | assayed_using(PomBase:SPBC582.03) | No | Yes |
| 17 | Reference | PMID:23697806 | Yes | No |
| 18 | taxon | taxon:4896 | Yes | No |
| 19 | Date | 2012-01-01 | Yes | No |
| 20 | Ploidy | homozygous diploid | No | No |
Notes:
Please include all 19 columns. If you have nothing to put in one of the non-mandatory columns, include the header and leave the column blank in the rest of the rows.
- Include the systematic ID for each gene. You can look up systematic IDs on gene pages, or refer to the file of all gene names from the dataset download page.
- For help finding suitable ontology (FYPO) terms to describe your phenotypes, see the FYPO summary page and the FAQ on browsing FYPO. If you can’t find a term you need, email the helpdesk for assistance; we can add new FYPO terms as needed.
- The allele description specifically describes the change; see table below.
- In the Expression column, use one of these values: ‘overexpression’, ‘knockdown’, ‘endogenous’, ‘null’, ‘not specified’. Deletions should always have ‘null’ expression.
- The Parental strain column is for the parental strain designation, such as 972 h-, 975 h+, etc. This column must be filled in, but you can use “unknown” if you don’t know the original background.
- Use the Strain name (background) column for a lab’s in-house name/ID/designation for the background strain (i.e. the derivative of the parental strain that has selectable marker alleles etc.). The description in the Genotype column should match this background strain.
- The Genotype description column is for alleles in the background, such as selectable markers; these details are optional. To avoid redundancy, do not repeat the allele of interest (from column 3 or 9) in the genotype column.
- Gene names are optional. If you include them, use standard names in column 8 (see gene pages or the file of All Gene Names from the dataset download page).
- Allele names are optional. If you include them, use column 9 for the preferred allele name, and put any alternative names in column 10.
- See note 9 above. Separate multiple entries with pipes (|).
- Allowed allele types, example descriptions, etc. are shown in the table below.
- For the Evidence column, we use a small selection from the Evidence Ontology (ECO). You are welcome to enquire with us in advance to find out which ECO terms/IDs fit your experiments, but we can accept files with brief descriptions (such as those in the Canto phenotype evidence option list), which curators will convert to ECO IDs.
- Similarly, Conditions use a small ontology maintained in-house by PomBase curators, and we can either advise you about which terms/IDs to use, or convert from text to IDs when we receive your file. Use multiple entries in cases where more than one condition detail applies at the same time (e.g. high temperature, minimal medium). Separate multiple entries with commas (,). Use separate lines if a phenotype is observed under more than one set of conditions (e.g. high and low temperature).
- Penetrance describes the proportion of a population that shows a cell-level phenotype. Use decimals, percents, or “high” (above 80%), “medium” (20-80%), or “low” (less than 20%). We will convert to suitable IDs for loading. Penetrance data will be displayed as annotation extensions on gene pages.
- Severity (formerly designated “expressivity) uses”high” (synonym: strong), “medium”, or “low” (synonym: weak). We will convert to suitable IDs for loading. Severity data will be displayed as annotation extensions on gene pages.
- The Extension column can be used to record when a mutation in one gene affects another gene or its product. For example, if a mutation in gene A decreases its ability to phosphorylate protein B, you can use the phenotype “decreased protein kinase activity” and put the ID for gene B in an extension. Multiple extensions can be included for a phenotype annotation. Separate extensions with a comma (,) if they combine to form a “compound” extension (two or more genes assayed together), or with a pipe (|) if they are independent. Most phenotype extensions will be independent and pipe-separated.
- The Reference column has the publication’s PubMed ID (PMID).
- The taxon will usually be 4896 (the NCBI taxon ID for Schizosaccharomyces pombe), although if you have an NCBI taxon ID for a specific S. pombe strain you are welcome to use it
- The date is the date on which the annotations are created; you may use the paper publication date or the date on which you prepare your data file. Format: YYYY-MM-DD
- We can currently capture only haploid and homozygous diploid datasets via PHAF files. Allowed values for this column are “haploid” and “homozygous diploid”. If the column is empty the dataset is assumed to be haploid. If you have a phenotype dataset for non-homozygous diploids please contact the Helpdesk
Details for allele types and descriptions:
General note: Nucleotide and amino acid positions should reflect the current sequence data in PomBase. Please refer to the Gene Coordinate Changes page to ensure that your residue position entries are up to date.
For protein-coding genes, number nucleotide residues from 1 starting with the A of the initiator ATG.
For histones, amino acid residue numbering assumes that the initiator methionine is removed.
| Allele type (col. 11) | Example allele description (col. 3) | Notes |
|---|---|---|
| amino acid mutation | S123A | use one-letter code; if more than one change, separate with comma(s) |
| deletion | deletion | use this description for complete deletions |
| nucleotide mutation | C123A | if more than one change, separate with comma(s) |
| disruption | pab1::ura4+ | expression will usually, but not always, be null |
| other | RGTPI inserted after I254 | include a brief text description |
| partial amino acid deletion | 1-100 or A123* | indicate deleted residues; use comma-separated ranges for discontinuous deleted segments; use * for nonsense mutations. |
| partial nucleotide deletion | 500-800 | indicate deleted residues; use comma-separated ranges for discontinuous deleted segments |
| unknown | unknown | an allele name is required if the type and description are unknown |
| wild type | wild type | use with altered expression (overexpression or knockdown) for single-allele phenotypes |
Please contact the PomBase curators if you have any questions about what to use for Evidence, Conditions, etc., or anything else you need to represent your data in this format.
Return to the Fission Yeast Phenotype Ontology page
GO Slims - Gene Ontology subsets
“GO slims” are subsets of the Gene Ontology (GO) that provide a broad overview of annotation distribution. Slims can offer a useful overview of a genome or the results of a large-scale experiment. For more information on GO slims, please see PomBase GO Slimming Tips and the GO Subset Guide at the Gene Ontology website.
PomBase provides a GO slim term set for each major branch of GO:
- GO molecular function slim term set
- GO biological process slim term set
- GO cellular component slim term set
Each fission yeast GO slim has been constructed to optimise coverage of gene products annotated to terms in the branch of GO. For the biological process and cellular component branches, coverage is almost complete; the molecular function branch has somewhat lower coverage. These slims provide good starting points for users who wish to identify terms of biological interest to create a “custom slim”, or to become familiar with the genome contents.
In the GO slim tables, GO IDs link to the QuickGO browser, where you can explore the ontology and annotations further. The annotation totals include annotations to the slim term and to descendants following the is_a, part_of, regulates, positively_regulates, and negatively_regulates relationships, and link to gene lists. (Note: the cellular component ontology does not contain any “regulates” links.)
The GO biological process slim table also includes links to visualisations in esyN for the physical interaction network of genes annotated to each term.
The bottom of each GO slim page lists some simple statistics: the total number of gene products annotated to slim terms, and the number of protein-coding gene products not covered by the slim, either because they are not annotated to any term in the GO branch, or because they have annotations to terms not covered by the slim.
Current GO slim IDs and term names can be downloaded from the PomBase ftp site:
Publication pages
For each publication loaded into PomBase, a page summarizes essential details about paper, and shows any annotations that cite it.
Publication details, including links to PubMed and EuropePMC
Any community curators who have contributed annotations via Canto are acknowledged.
Summary views are identical to those on gene pages (GO example).
In detailed views annotations are displayed as on gene pages, except that a column for the annotated gene is included and the Reference column is omitted.
Term and evidence filtering are available for phenotype annotations as described in the gene page documentation.
Like gene pages, publication pages include annotations of all types, with summary and detailed views available for most types:
Qualitative gene expression bulk upload file format
PomBase welcomes submissions of published large-scale gene expression data sets. We have devised a tab-delimited text file format for bulk data representing qualitative assessments of protein or RNA levels.
Note: Please use this format only for data that you want to appear in the “Qualitative gene expression” section of PomBase gene pages. If you have gene expression data that should be included as a data track in the PomBase genome browser (microarray, RNASeq, etc.), please use the data submission form for HTP sequence-linked data.
Include a header line that labels the columns – use the entry in the Contents column below as the column header text.
| Column | Contents | Example | Mandatory? | Multiple entries allowed? |
|---|---|---|---|---|
| 1 | Gene systematic ID | SPBC11B10.09 | Yes | No |
| 2 | Gene name | cdc2 | No | No |
| 3 | Type | protein | Yes | No |
| 4 | Evidence | ECO:0000006 | Yes | No |
| 5 | Qualifier | increased | Yes | No |
| 6 | Extension | during(GO:0000084) | Yes | Yes |
| 7 | Reference | PMID:18203864 | Yes | No |
| 8 | Taxon | 4896 | Yes | No |
| 9 | Date | 2014-05-01 | Yes | No |
- Include the systematic ID for each gene. You can look up systematic IDs on gene pages, or refer to the file of all gene names from the dataset download page.
- Gene names are optional. If you include them, use standard names in column 2 (see gene pages or the file of all gene names from the dataset download page.
- Type: what was measured; use “RNA” or “protein”
- For the Evidence column, we use a small selection from the Evidence Ontology (ECO). You are welcome to enquire with us in advance to find out which ECO terms/IDs fit your experiments, but we can accept files with brief descriptions, which curators will convert to ECO IDs.
- The Qualifier column uses a small vocabulary to describe what is observed about the RNA or protein level. Use one of: present, absent, unchanged, increased, decreased, constant, fluctuates
- The Extension column documents circumstances under which the RNA or protein level is observed (or changes). Follow one of these patterns:
- “during(GO:0000084)” - when a specific biological process, such as a response to a stimulus, is taking place, or during a cell cycle phase
- “in_presence_of(CHEBI:18420)” - when a specific chemical substance is present
- “in_absence_of(CHEBI:18420)” - when a specific chemical substance is absent
- “occurs_in(GO:0005634)” - when the level is observed in part, rather than all, of a cell
- The Reference column has the publication’s PubMed ID (PMID).
- The taxon will usually be 4896 (the NCBI taxon ID for Schizosaccharomyces pombe), although if you have an NCBI taxon ID for a specific S. pombe strain you are welcome to use it
- The date is the date on which the annotations are created; you may use the paper publication date or the date on which you prepare your data file. Format: YYYY-MM-DD
Quantitative gene expression bulk upload file format
PomBase welcomes submissions of published large-scale gene expression data sets. We have devised a tab-delimited text file format for bulk data representing representing protein or RNA copy number per cell.
Note: Please use this format only for data that you want to appear in the “Quantitative gene expression” section of PomBase gene pages. If you have gene expression data that should be included as a data track in the PomBase genome browser (microarray, RNASeq, etc.), please use the data submission form for HTP sequence-linked data.
Include a header line that labels the columns – use the entry in the Contents column below as the column header text.
| Column | Contents | Example | Mandatory? | Multiple entries allowed? |
|---|---|---|---|---|
| 1 | Gene systematic ID | SPBC11B10.09 | Yes | No |
| 2 | Gene name | cdc2 | No | No |
| 3 | Type | protein | Yes | No |
| 4 | Extension | during(GO:0051329) | No | No |
| 5 | Copies per cell | 1234 | Yes | No |
| 6 | Range | 1100-1350 | No | No |
| 7 | Evidence | ECO:0000006 | Yes | No |
| 8 | Scale | single_cell | Yes | No |
| 9 | Condition | minimal medium, high temperature | Yes | Yes |
| 10 | Reference | PMID:23101633 | Yes | No |
| 11 | Taxon | 4896 | Yes | No |
| 12 | Date | 2014-05-01 | Yes | No |
- Include the systematic ID for each gene. You can look up systematic IDs on gene pages, or refer to the file of all gene names from the dataset download page.
- Gene names are optional. If you include them, use standard names in column 2 (see gene pages or the file of all gene names from the dataset download page.
- Type: what was measured; use “RNA” or “protein”
- The Extension column documents circumstances under which the RNA or protein level is observed (or changes). Follow one of these patterns: “during (GO:0000084)” - when a specific biological process, such as a response to a stimulus, is taking place, or during a cell cycle phase; “in_presence_of(CHEBI:18420)” - when a specific chemical substance is present; “occurs_in(GO:0005634)” when the level is observed in part, rather than all, of a cell.
- Copies per cell: can be an average
- Range: optional; use if the experimental method yields a range of copies/cell
- For the Evidence column, we use a small selection from the Evidence Ontology (ECO). You are welcome to enquire with us in advance to find out which ECO terms/IDs fit your experiments, but we can accept files with brief descriptions, which curators will convert to ECO IDs.
- Scale: whether levels are determined for a single cell or a cell population as a whole; use “single_cell” or “population”
- Conditions use a small ontology maintained in-house by PomBase curators, and we can either advise you about which terms/IDs to use, or convert from text to IDs when we receive your file.
- The Reference column has the publication’s PubMed ID (PMID).
- The taxon will usually be 4896 (the NCBI taxon ID for Schizosaccharomyces pombe), although if you have an NCBI taxon ID for a specific S. pombe strain you are welcome to use it
- The date is the date on which the annotations are created; you may use the paper publication date or the date on which you prepare your data file. Format: YYYY-MM-DD
Quick Little Tool
PomBase’s Quick Little Tool (QuiLT) allows you to view multiple types of annotation for genes in a list in a single graphical display.
Finding QuiLT
On any gene list page, including Advanced Search results and the gene lists linked to ontology term pages, click the “Visualise” button to reach QuiLT. To return to the previous page, use the “Finish visualisation” button.
Adding and sorting annotations
In the QuiLT display, each row represents a single gene, and each column is an annotation type.
Use the checkboxes (1) to toggle an annotation type on and off. When annotations are shown, a link appears to sort on that annotation type. You may want to try different combinations of which types are shown, and which used to sort the list, until you get a display you like. You can download the graph (with key) in SVG format at any time (2). The key (4) shows only terms used to annotate genes in the list, so for small gene lists not all terms may appear.
Click on a row to select a single gene, or click on a box in any column (3) to select all genes in it. In the displayed gene list, you can clear the selection (5) or use the “Filter” button (6) to create a new gene list from the selection (which you can then visualise in QuiLT).
Sharing results
Each QuiLT visualisation page has a stable, unique URL that you can bookmark, copy/paste, and share. Anyone who follows a shared link will see QuiLT displaying the same gene list. Clicking the “Advanced Search” button adds a query that would produce the gene list to the query history.
Available annotation types
At present, QuiLT includes:
- Deletion viability
- Presence or absence of budding yeast orthologs
- Presence or absence of human orthologs
- Presence or absence of transmembrane domains
- GO biological process
- GO cellular component
- GO molecular function
- Characterization status for protein-coding genes
- Taxonomic distribution
- Protein length
GO annotation precedence
In each branch of GO, only one term per gene can be included for display. If a gene is annotated to more than one GO term, one is selected for the QuiLT display according to a set order of precedence:
- GO biological process
- signaling (GO:0023052)
- gene expression (GO:0010467)
- chromatin organization (GO:0006325)
- protein folding (GO:0006457)
- cellular component biogenesis (GO:0044085)
- DNA metabolic process (GO:0006259)
- cell cycle (GO:0007049)
- cytoskeleton organization (GO:0007010)
- membrane organization (GO:0061024)
- organelle localization (GO:0051640)
- lipid metabolic process (GO:0006629)
- small molecule metabolic process (GO:0044281)
- generation of precursor metabolites and energy (GO:0006091)
- transport (GO:0006810)
- cellular catabolic process (GO:0044248)
- detoxification (GO:0098754)
- other (i.e none of the above)
- unknown
- GO cellular component
- nucleus (GO:0005634)
- endoplasmic reticulum (ER; GO:0005783)
- mitochondrion (GO:0005739)
- cytoplasm (GO:0005737)
- other (i.e none of the above)
- unknown
- GO molecular function
- oxidoreductase activity (GO:0016491)
- hydrolase activity (GO:0016787)
- transferase activity (GO:0016740)
- ligase activity (GO:0016874)
- cyclase activity (GO:0009975)
- lyase activity (GO:0016829)
- other catalytic activity (any other descendant of GO:0003824)
- molecular adaptor activity (GO:0060090)
- enzyme regulator activity (GO:0030234)
- DNA binding (GO:0003677)
- transcription regulator activity (GO:0140110)
- transporter activity (GO:0005215)
- cytoskeletal protein binding (GO:0008092)
- unfolded protein binding (GO:0051082)
- RNA binding (GO:0003723)
- metal ion binding (GO:0046872)
- lipid binding (GO:0008289)
- cell adhesion mediator activity (GO:0098631)
- structural molecule activity (GO:0005198)
- other (i.e none of the above)
- unknown
Simple search
The simple search is available via the search box in the header on every PomBase page:
The simple search works for:
- Fission yeast gene names, synonyms, and systematic IDs
- Fission yeast gene product descriptions
- Human orthologs of fission yeast genes — search by standard gene symbols
- Budding yeast orthologs of fission yeast genes — search by standard gene names, ORF names, or SGD IDs
- Publications — search by PubMed ID
- Ontology terms — search by term ID
Start typing to see a pulldown of autocomplete matches, then choose one, or if there is a single match simply hit return, to go to the matching gene page.
For publications or ontology terms, type or paste an ID as directed. If no autocomplete suggestions appear, enter the ID and hit return to execute the search.
Taxonomic conservation
The Taxonomic conservation section provides manually assigned classifiers of taxon distribution (at the domain/kingdom level) of the product of a protein-coding gene. The classifiers come from a small controlled vocabulary maintained by PomBase curators. All applicable terms are assigned to a protein.
For each annotation, the summary view shows a text description, which corresponds to an entry in the internal PBO term set. The detailed view adds the PBO ID and a count that links to the ontology term page for the description.
Taxonomic conservation terms
- These terms identify the taxonomic groups in which gene product ortholog(s) have been identified:
- conserved in archaea
- conserved in bacteria
- conserved in eukaryotes
- conserved in fungi
- conserved in metazoa
- conserved in vertebrates
- These two terms represent taxon restrictions, and indicate that a gene product has not been detected outside these taxa:
- conserved in fungi only
- conserved in eukaryotes only
- Other terms
- Schizosaccharomyces specific - indicates that a gene product is only identified in the genus Schizosaccharomyces at present, but is present in more than one species in this genus
- Schizosaccharomyces pombe specific - indicates that a gene product is identified only in S. pombe, not in any other species even in the Schizosaccharomyces genus
- no apparent S. cerevisiae ortholog - indicates a gene product which is conserved at least outside the Schizosaccharomyces but is absent from S. cerevisiae
- faster evolving duplicate - indicates that the copy of a gene product which has duplicated after the divergence of Schizosaccharomyces from other yeasts is evolving faster than its duplicate partner (judged because the fission yeast duplicate is more closely related to the orthologs in other species, but is the best hit of this gene product)
- predominantly single copy (one to one) - the gene product is conserved largely one-to one across species with minor exceptions (for example, frequently duplicated in the vertebrate lineage)
- orthologs cannot be distinguished - the gene product appears to be conserved, but it is not possible to identify orthologs unambiguously
Additional notes:
- Any term which has “conserved in fungi” but does not have “no apparent S. cerevisiae ortholog” will have a manually annotated S. cerevisiae ortholog.
- Any gene product which is annotated as “conserved in vertebrates” will have a manually annotated human ortholog.
